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The title compound, abbreviated as 5'ThiomethylImmA, is a potent inhibitor of methylthioadenosine phosphorylase [Singh et al. (2004). Biochemistry, 43, 9-18]. The synchrotron study reported here shows that the hydrochloride salt crystallizes with two independent, nearly superimposable, dications as a monohydrate with formula 2C12H19N5O2S2+·4Cl-·H2O. Hydrogen bonding utilizing the H atoms of the dication is found to favour certain molecular conformations in the salt, which are significantly different from those found as bound in the enzyme. Ligand docking studies starting from either of these dications or related neutral structures successfully place the conformationally revised structures in the enzyme active site but only under particular hydrogen-bonding and molecular flexibility criteria. Density functional theory calculations verify the energy similarity of the independent cations and confirm the significant energy cost of the required conformational change to the enzyme bound form. The results suggest that using crystallographically determined free ligand coordinates as starting parameters for modelling may have serious limitations.
Supporting information
CCDC reference: 804121
The compound was prepared as reported for compound 2 by Evans et al.
(2004).
The N—H distances of two types (viz. N3, N7, N13, N17 and N6, N16)
were restrained to be equal [SHELXL (Sheldrick, 2008) SADI
function
with effective standard deviation of 0.03 Å]. The methyl H atoms were
constrained to an ideal geometry (C—H = 0.98 Å) but were allowed to rotate
freely about the adjacent C—C bond. The hydroxyl H atoms were constrained to
an ideal geometry (O—H = 0.84 Å) with Uiso(H) =
1.2Ueq(O), but were allowed to rotate freely about the adjacent C—O
bond. All other H atoms were placed in geometrically idealized positions and
constrained to ride on their parent atoms with C—H distances of 1.00
(primary), 0.99 (methylene) or 0.95 (aromatic) Å. All H atoms were refined
with Uiso(H) = 1.2Ueq(parent atom).
Data collection: DENZO (Otwinowski & Minor, 1997); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
Bis[(1
S)-1,4-azanediyl-1-(9-deazaadenin-9-yl)-1,4-dideoxy-5-
methylsulfanyl-D-ribitol] tetrakis(hydrochloride) monohydrate
top
Crystal data top
2C12H19N5O2S2+·4Cl−·H2O | F(000) = 1576 |
Mr = 754.58 | Dx = 1.539 Mg m−3 |
Orthorhombic, P212121 | Synchrotron radiation, λ = 0.92014 Å |
Hall symbol: P 2ac 2ab | θ = 3.8–26.5° |
a = 7.0080 (14) Å | µ = 1.05 mm−1 |
b = 18.717 (4) Å | T = 100 K |
c = 24.825 (5) Å | Plate, colourless |
V = 3256.3 (11) Å3 | 0.23 × 0.20 × 0.15 mm |
Z = 4 | |
Data collection top
ADSC Quantum CCD Detector diffractometer | 3821 reflections with I > 2σ(I) |
Si111 monochromator | Rint = 0.000 |
Detector resolution: 4000 pixels mm-1 | θmax = 29.6°, θmin = 1.8° |
ϕ scan | h = −6→6 |
3864 measured reflections | k = −19→19 |
3864 independent reflections | l = −25→25 |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.027 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.066 | w = 1/[σ2(Fo2) + (0.P)2 + 2.896P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max = 0.001 |
3864 reflections | Δρmax = 0.40 e Å−3 |
454 parameters | Δρmin = −0.24 e Å−3 |
12 restraints | Absolute structure: Flack (1983), ???? Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: −0.03 (3) |
Crystal data top
2C12H19N5O2S2+·4Cl−·H2O | V = 3256.3 (11) Å3 |
Mr = 754.58 | Z = 4 |
Orthorhombic, P212121 | Synchrotron radiation, λ = 0.92014 Å |
a = 7.0080 (14) Å | µ = 1.05 mm−1 |
b = 18.717 (4) Å | T = 100 K |
c = 24.825 (5) Å | 0.23 × 0.20 × 0.15 mm |
Data collection top
ADSC Quantum CCD Detector diffractometer | 3821 reflections with I > 2σ(I) |
3864 measured reflections | Rint = 0.000 |
3864 independent reflections | θmax = 29.6° |
Refinement top
R[F2 > 2σ(F2)] = 0.027 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.066 | Δρmax = 0.40 e Å−3 |
S = 1.06 | Δρmin = −0.24 e Å−3 |
3864 reflections | Absolute structure: Flack (1983), ???? Friedel pairs |
454 parameters | Absolute structure parameter: −0.03 (3) |
12 restraints | |
Special details top
Experimental. Crystal decay was monitored and corrected by the inter-frame analysis
(DENZO: Otwinowski & Minor,1997). |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell e.s.d.'s are taken
into account individually in the estimation of e.s.d.'s in distances, angles
and torsion angles; correlations between e.s.d.'s in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s.
planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor
wR and goodness of fit S are based on F2, conventional
R-factors R are based on F, with F set to zero for
negative F2. The threshold expression of F2 >
σ(F2) is used only for calculating R-factors(gt) etc.
and is not relevant to the choice of reflections for refinement.
R-factors based on F2 are statistically about twice as large
as those based on F, and R- factors based on ALL data will be
even larger. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
Cl1 | 0.55979 (11) | 0.32882 (4) | 0.05394 (3) | 0.0173 (2) | |
Cl2 | 0.11689 (12) | 0.60238 (4) | 0.06993 (3) | 0.01837 (19) | |
Cl3 | 0.48675 (12) | 0.71937 (4) | 0.26035 (3) | 0.0221 (2) | |
Cl4 | 0.98911 (13) | 0.71774 (4) | 0.21636 (3) | 0.0244 (2) | |
S1 | 0.59682 (13) | 0.54848 (4) | 0.48204 (3) | 0.0197 (2) | |
O2' | 1.1834 (3) | 0.71312 (11) | 0.39562 (8) | 0.0206 (5) | |
H2O' | 1.2315 | 0.7479 | 0.4122 | 0.025* | |
O3' | 0.9786 (3) | 0.59735 (11) | 0.35863 (8) | 0.0195 (5) | |
H3O' | 1.0979 | 0.6008 | 0.3564 | 0.023* | |
N1' | 0.6702 (4) | 0.71542 (13) | 0.37482 (11) | 0.0140 (6) | |
H1N' | 0.617 (5) | 0.7453 (16) | 0.3985 (13) | 0.017* | |
H2N' | 0.611 (5) | 0.7137 (16) | 0.3455 (13) | 0.017* | |
N1 | 0.7641 (4) | 0.97655 (13) | 0.24214 (10) | 0.0166 (7) | |
N3 | 0.7974 (4) | 0.85403 (13) | 0.26189 (9) | 0.0156 (6) | |
H3N | 0.812 (5) | 0.8125 (13) | 0.2486 (12) | 0.019* | |
N6 | 0.8211 (4) | 1.06371 (14) | 0.30589 (11) | 0.0201 (7) | |
H6A | 0.833 (5) | 1.0948 (15) | 0.2822 (11) | 0.024* | |
H6B | 0.860 (5) | 1.0738 (17) | 0.3369 (10) | 0.024* | |
N7 | 0.8772 (4) | 0.94027 (13) | 0.38524 (10) | 0.0138 (6) | |
H7N | 0.880 (5) | 0.9794 (13) | 0.4007 (12) | 0.017* | |
C1' | 0.8664 (5) | 0.74539 (15) | 0.36206 (11) | 0.0152 (7) | |
H1' | 0.9086 | 0.7266 | 0.3263 | 0.018* | |
C2' | 0.9867 (5) | 0.71000 (16) | 0.40637 (11) | 0.0155 (7) | |
H2' | 0.9586 | 0.7326 | 0.4420 | 0.019* | |
C3' | 0.9140 (5) | 0.63388 (15) | 0.40564 (11) | 0.0141 (7) | |
H3' | 0.9498 | 0.6077 | 0.4393 | 0.017* | |
C4' | 0.6980 (5) | 0.64113 (15) | 0.40005 (11) | 0.0127 (7) | |
H4' | 0.6493 | 0.6038 | 0.3747 | 0.015* | |
C5' | 0.5877 (5) | 0.63705 (15) | 0.45291 (11) | 0.0148 (7) | |
H5A' | 0.4529 | 0.6504 | 0.4464 | 0.018* | |
H5B' | 0.6420 | 0.6718 | 0.4787 | 0.018* | |
C6' | 0.4043 (7) | 0.50575 (18) | 0.44716 (15) | 0.0395 (11) | |
H6A' | 0.2849 | 0.5311 | 0.4548 | 0.047* | |
H6B' | 0.3934 | 0.4561 | 0.4593 | 0.047* | |
H6C' | 0.4292 | 0.5067 | 0.4083 | 0.047* | |
C2 | 0.7630 (5) | 0.90827 (16) | 0.22861 (12) | 0.0184 (8) | |
H2 | 0.7354 | 0.8970 | 0.1921 | 0.022* | |
C4 | 0.8305 (4) | 0.86900 (15) | 0.31516 (11) | 0.0119 (7) | |
C5 | 0.8350 (4) | 0.94007 (15) | 0.33133 (11) | 0.0125 (7) | |
C6 | 0.8083 (5) | 0.99495 (15) | 0.29388 (12) | 0.0137 (7) | |
C8 | 0.8937 (5) | 0.87214 (15) | 0.40235 (12) | 0.0142 (7) | |
H8 | 0.9210 | 0.8584 | 0.4384 | 0.017* | |
C9 | 0.8651 (5) | 0.82491 (15) | 0.35997 (11) | 0.0129 (7) | |
S2 | 0.13315 (12) | 0.87798 (4) | 0.06431 (3) | 0.0192 (2) | |
O12' | 0.8105 (3) | 0.72051 (10) | 0.04478 (8) | 0.0166 (5) | |
H12O | 0.8701 | 0.6837 | 0.0544 | 0.020* | |
O13' | 0.6907 (3) | 0.83507 (10) | 0.10569 (8) | 0.0168 (5) | |
H13O | 0.7895 | 0.8400 | 0.0869 | 0.020* | |
N11' | 0.4061 (4) | 0.70763 (13) | 0.13602 (11) | 0.0135 (6) | |
H11A | 0.314 (5) | 0.6788 (17) | 0.1206 (12) | 0.016* | |
H11B | 0.385 (5) | 0.7048 (15) | 0.1711 (13) | 0.016* | |
N11 | 0.7402 (4) | 0.45557 (13) | 0.24352 (9) | 0.0139 (6) | |
N13 | 0.7216 (4) | 0.57741 (13) | 0.21988 (10) | 0.0145 (6) | |
H13N | 0.750 (5) | 0.6212 (13) | 0.2276 (12) | 0.017* | |
N16 | 0.6765 (4) | 0.36652 (14) | 0.18173 (10) | 0.0171 (7) | |
H61A | 0.651 (5) | 0.3518 (16) | 0.1503 (10) | 0.020* | |
H61B | 0.673 (5) | 0.3380 (15) | 0.2067 (11) | 0.020* | |
N17 | 0.6078 (4) | 0.48691 (13) | 0.10073 (10) | 0.0143 (6) | |
H17N | 0.600 (5) | 0.4500 (14) | 0.0820 (11) | 0.017* | |
C11' | 0.6048 (5) | 0.68262 (15) | 0.12097 (11) | 0.0129 (7) | |
H11' | 0.6990 | 0.7042 | 0.1465 | 0.016* | |
C12' | 0.6252 (5) | 0.71856 (15) | 0.06594 (11) | 0.0134 (7) | |
H12' | 0.5381 | 0.6947 | 0.0396 | 0.016* | |
C13' | 0.5544 (4) | 0.79442 (15) | 0.07684 (11) | 0.0132 (7) | |
H13' | 0.5157 | 0.8189 | 0.0427 | 0.016* | |
C14' | 0.3823 (5) | 0.78349 (15) | 0.11466 (11) | 0.0139 (7) | |
H14' | 0.3902 | 0.8181 | 0.1453 | 0.017* | |
C15' | 0.1870 (5) | 0.78941 (16) | 0.08794 (12) | 0.0168 (7) | |
H15A | 0.0880 | 0.7747 | 0.1141 | 0.020* | |
H15B | 0.1818 | 0.7559 | 0.0571 | 0.020* | |
C16' | 0.1406 (6) | 0.92665 (17) | 0.12637 (13) | 0.0308 (9) | |
H16A | 0.0793 | 0.8985 | 0.1548 | 0.037* | |
H16B | 0.0730 | 0.9721 | 0.1220 | 0.037* | |
H16C | 0.2737 | 0.9360 | 0.1362 | 0.037* | |
C12 | 0.7560 (5) | 0.52407 (16) | 0.25467 (12) | 0.0187 (8) | |
H12 | 0.7947 | 0.5367 | 0.2901 | 0.022* | |
C14 | 0.6696 (4) | 0.56097 (15) | 0.16816 (11) | 0.0109 (7) | |
C15 | 0.6584 (4) | 0.48961 (15) | 0.15404 (12) | 0.0115 (7) | |
C16 | 0.6895 (5) | 0.43535 (15) | 0.19256 (11) | 0.0121 (7) | |
C18 | 0.5854 (5) | 0.55487 (15) | 0.08232 (11) | 0.0139 (7) | |
H18 | 0.5497 | 0.5673 | 0.0466 | 0.017* | |
C19 | 0.6222 (4) | 0.60331 (15) | 0.12306 (11) | 0.0104 (7) | |
O1W | 0.3501 (4) | 0.58651 (13) | 0.32748 (9) | 0.0245 (6) | |
H1WA | 0.335 (5) | 0.5442 (18) | 0.3059 (14) | 0.029* | |
H2WA | 0.377 (6) | 0.6195 (19) | 0.3085 (14) | 0.029* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Cl1 | 0.0234 (5) | 0.0125 (4) | 0.0160 (4) | −0.0001 (3) | 0.0001 (3) | 0.0006 (3) |
Cl2 | 0.0210 (5) | 0.0126 (4) | 0.0215 (4) | 0.0011 (3) | −0.0033 (3) | 0.0003 (3) |
Cl3 | 0.0320 (6) | 0.0196 (4) | 0.0146 (4) | 0.0029 (4) | −0.0022 (3) | −0.0023 (3) |
Cl4 | 0.0273 (5) | 0.0207 (4) | 0.0251 (4) | 0.0020 (4) | 0.0023 (3) | −0.0033 (3) |
S1 | 0.0290 (6) | 0.0134 (4) | 0.0166 (4) | −0.0005 (4) | 0.0014 (4) | 0.0029 (3) |
O2' | 0.0208 (16) | 0.0166 (12) | 0.0244 (12) | −0.0011 (10) | −0.0016 (10) | −0.0041 (9) |
O3' | 0.0233 (15) | 0.0147 (11) | 0.0204 (11) | −0.0036 (11) | 0.0052 (10) | −0.0045 (9) |
N1' | 0.0199 (19) | 0.0114 (14) | 0.0106 (13) | −0.0038 (13) | −0.0019 (11) | 0.0004 (11) |
N1 | 0.0188 (19) | 0.0163 (15) | 0.0148 (14) | 0.0004 (11) | 0.0055 (11) | 0.0005 (11) |
N3 | 0.0215 (18) | 0.0092 (14) | 0.0159 (14) | −0.0013 (12) | 0.0022 (12) | 0.0001 (12) |
N6 | 0.031 (2) | 0.0112 (16) | 0.0180 (15) | −0.0002 (13) | 0.0026 (13) | 0.0036 (12) |
N7 | 0.0168 (17) | 0.0077 (14) | 0.0169 (15) | −0.0032 (12) | 0.0006 (12) | −0.0027 (11) |
C1' | 0.021 (2) | 0.0101 (17) | 0.0148 (15) | −0.0013 (15) | −0.0029 (14) | −0.0014 (12) |
C2' | 0.013 (2) | 0.0190 (17) | 0.0146 (16) | −0.0006 (15) | −0.0003 (13) | −0.0021 (13) |
C3' | 0.024 (2) | 0.0081 (16) | 0.0108 (15) | 0.0031 (14) | −0.0010 (13) | −0.0023 (12) |
C4' | 0.019 (2) | 0.0079 (15) | 0.0112 (15) | 0.0002 (14) | −0.0013 (13) | 0.0021 (12) |
C5' | 0.018 (2) | 0.0124 (16) | 0.0137 (15) | 0.0012 (14) | −0.0005 (13) | 0.0023 (12) |
C6' | 0.061 (3) | 0.025 (2) | 0.032 (2) | −0.021 (2) | −0.017 (2) | 0.0056 (16) |
C2 | 0.022 (2) | 0.020 (2) | 0.0133 (16) | −0.0009 (15) | −0.0003 (13) | 0.0025 (14) |
C4 | 0.009 (2) | 0.0122 (17) | 0.0148 (17) | −0.0042 (14) | 0.0005 (12) | 0.0003 (13) |
C5 | 0.006 (2) | 0.0147 (17) | 0.0167 (18) | −0.0025 (13) | 0.0010 (12) | 0.0002 (13) |
C6 | 0.008 (2) | 0.0138 (18) | 0.0192 (18) | −0.0012 (13) | 0.0037 (13) | 0.0010 (13) |
C8 | 0.0142 (19) | 0.0125 (17) | 0.0157 (16) | 0.0001 (14) | −0.0017 (14) | 0.0003 (13) |
C9 | 0.012 (2) | 0.0096 (16) | 0.0177 (16) | −0.0049 (14) | −0.0002 (13) | 0.0016 (13) |
S2 | 0.0239 (5) | 0.0153 (4) | 0.0182 (4) | 0.0030 (4) | −0.0027 (3) | 0.0011 (3) |
O12' | 0.0149 (14) | 0.0150 (11) | 0.0199 (11) | 0.0034 (10) | 0.0025 (9) | 0.0038 (9) |
O13' | 0.0147 (14) | 0.0134 (11) | 0.0223 (11) | −0.0049 (10) | 0.0011 (9) | −0.0023 (9) |
N11' | 0.0157 (18) | 0.0130 (15) | 0.0118 (13) | −0.0002 (12) | 0.0033 (12) | 0.0021 (11) |
N11 | 0.0192 (18) | 0.0120 (15) | 0.0104 (13) | 0.0022 (11) | −0.0037 (11) | 0.0002 (11) |
N13 | 0.0223 (17) | 0.0088 (14) | 0.0124 (14) | 0.0000 (12) | −0.0051 (11) | −0.0025 (11) |
N16 | 0.025 (2) | 0.0108 (16) | 0.0150 (15) | −0.0015 (13) | 0.0016 (12) | 0.0045 (11) |
N17 | 0.0200 (17) | 0.0101 (14) | 0.0129 (14) | −0.0008 (12) | 0.0001 (12) | −0.0032 (10) |
C11' | 0.014 (2) | 0.0115 (16) | 0.0132 (15) | −0.0003 (14) | −0.0018 (13) | −0.0014 (12) |
C12' | 0.016 (2) | 0.0130 (16) | 0.0111 (15) | −0.0007 (14) | 0.0007 (13) | 0.0010 (12) |
C13' | 0.016 (2) | 0.0118 (16) | 0.0121 (15) | 0.0008 (13) | −0.0023 (12) | −0.0010 (12) |
C14' | 0.018 (2) | 0.0094 (15) | 0.0139 (15) | 0.0041 (15) | −0.0002 (13) | −0.0011 (12) |
C15' | 0.019 (2) | 0.0119 (16) | 0.0189 (17) | 0.0008 (15) | 0.0014 (14) | 0.0015 (13) |
C16' | 0.049 (3) | 0.0194 (19) | 0.0241 (19) | 0.0061 (18) | 0.0000 (17) | −0.0071 (14) |
C12 | 0.023 (2) | 0.021 (2) | 0.0126 (17) | 0.0065 (15) | 0.0008 (13) | 0.0010 (14) |
C14 | 0.008 (2) | 0.0122 (16) | 0.0123 (17) | 0.0026 (13) | 0.0038 (12) | −0.0023 (12) |
C15 | 0.004 (2) | 0.0138 (17) | 0.0167 (18) | 0.0016 (13) | 0.0035 (12) | 0.0000 (13) |
C16 | 0.008 (2) | 0.0129 (18) | 0.0158 (17) | 0.0031 (13) | 0.0032 (13) | 0.0027 (13) |
C18 | 0.016 (2) | 0.0126 (17) | 0.0126 (16) | 0.0032 (14) | 0.0006 (13) | 0.0018 (13) |
C19 | 0.0075 (19) | 0.0112 (16) | 0.0127 (16) | −0.0002 (14) | 0.0034 (12) | −0.0010 (12) |
O1W | 0.0271 (17) | 0.0217 (13) | 0.0246 (13) | −0.0048 (12) | 0.0000 (10) | −0.0041 (10) |
Geometric parameters (Å, º) top
S1—C6' | 1.792 (4) | S2—C15' | 1.798 (3) |
S1—C5' | 1.810 (3) | O12'—C12' | 1.401 (4) |
O2'—C2' | 1.405 (4) | O12'—H12O | 0.8400 |
O2'—H2O' | 0.8400 | O13'—C13' | 1.416 (4) |
O3'—C3' | 1.426 (3) | O13'—H13O | 0.8400 |
O3'—H3O' | 0.8400 | N11'—C11' | 1.516 (4) |
N1'—C1' | 1.519 (4) | N11'—C14' | 1.525 (4) |
N1'—C4' | 1.537 (4) | N11'—H11A | 0.92 (3) |
N1'—H1N' | 0.89 (3) | N11'—H11B | 0.88 (3) |
N1'—H2N' | 0.84 (3) | N11—C12 | 1.316 (4) |
N1—C2 | 1.321 (4) | N11—C16 | 1.367 (4) |
N1—C6 | 1.365 (4) | N13—C12 | 1.342 (4) |
N3—C2 | 1.331 (4) | N13—C14 | 1.370 (4) |
N3—C4 | 1.371 (4) | N13—H13N | 0.87 (2) |
N3—H3N | 0.85 (2) | N16—C16 | 1.319 (4) |
N6—C6 | 1.324 (4) | N16—H61A | 0.85 (2) |
N6—H6A | 0.83 (2) | N16—H61B | 0.82 (2) |
N6—H6B | 0.84 (2) | N17—C18 | 1.361 (4) |
N7—C8 | 1.349 (4) | N17—C15 | 1.371 (4) |
N7—C5 | 1.371 (4) | N17—H17N | 0.83 (2) |
N7—H7N | 0.83 (2) | C11'—C19 | 1.490 (4) |
C1'—C9 | 1.489 (4) | C11'—C12' | 1.529 (4) |
C1'—C2' | 1.536 (4) | C11'—H11' | 1.0000 |
C1'—H1' | 1.0000 | C12'—C13' | 1.528 (4) |
C2'—C3' | 1.513 (4) | C12'—H12' | 1.0000 |
C2'—H2' | 1.0000 | C13'—C14' | 1.542 (4) |
C3'—C4' | 1.527 (5) | C13'—H13' | 1.0000 |
C3'—H3' | 1.0000 | C14'—C15' | 1.525 (4) |
C4'—C5' | 1.525 (4) | C14'—H14' | 1.0000 |
C4'—H4' | 1.0000 | C15'—H15A | 0.9900 |
C5'—H5A' | 0.9900 | C15'—H15B | 0.9900 |
C5'—H5B' | 0.9900 | C16'—H16A | 0.9800 |
C6'—H6A' | 0.9800 | C16'—H16B | 0.9800 |
C6'—H6B' | 0.9800 | C16'—H16C | 0.9800 |
C6'—H6C' | 0.9800 | C12—H12 | 0.9500 |
C2—H2 | 0.9500 | C14—C15 | 1.383 (4) |
C4—C5 | 1.390 (4) | C14—C19 | 1.411 (4) |
C4—C9 | 1.406 (4) | C15—C16 | 1.412 (4) |
C5—C6 | 1.398 (4) | C18—C19 | 1.382 (4) |
C8—C9 | 1.389 (4) | C18—H18 | 0.9500 |
C8—H8 | 0.9500 | O1W—H1WA | 0.96 (4) |
S2—C16' | 1.791 (3) | O1W—H2WA | 0.80 (4) |
| | | |
C6'—S1—C5' | 100.90 (16) | C12'—O12'—H12O | 109.5 |
C2'—O2'—H2O' | 109.5 | C13'—O13'—H13O | 109.5 |
C3'—O3'—H3O' | 109.5 | C11'—N11'—C14' | 107.6 (2) |
C1'—N1'—C4' | 107.7 (2) | C11'—N11'—H11A | 111 (2) |
C1'—N1'—H1N' | 106 (2) | C14'—N11'—H11A | 108.9 (19) |
C4'—N1'—H1N' | 110.5 (19) | C11'—N11'—H11B | 112 (2) |
C1'—N1'—H2N' | 106 (2) | C14'—N11'—H11B | 112.3 (19) |
C4'—N1'—H2N' | 112 (2) | H11A—N11'—H11B | 105 (3) |
H1N'—N1'—H2N' | 113 (3) | C12—N11—C16 | 119.1 (2) |
C2—N1—C6 | 119.0 (3) | C12—N13—C14 | 118.9 (3) |
C2—N3—C4 | 118.3 (3) | C12—N13—H13N | 121 (2) |
C2—N3—H3N | 119 (2) | C14—N13—H13N | 119 (2) |
C4—N3—H3N | 123 (2) | C16—N16—H61A | 121 (2) |
C6—N6—H6A | 122 (2) | C16—N16—H61B | 119 (2) |
C6—N6—H6B | 117 (2) | H61A—N16—H61B | 119 (3) |
H6A—N6—H6B | 117 (3) | C18—N17—C15 | 108.6 (2) |
C8—N7—C5 | 108.9 (2) | C18—N17—H17N | 126 (2) |
C8—N7—H7N | 134 (2) | C15—N17—H17N | 126 (2) |
C5—N7—H7N | 117 (2) | C19—C11'—N11' | 112.0 (3) |
C9—C1'—N1' | 111.8 (3) | C19—C11'—C12' | 117.5 (2) |
C9—C1'—C2' | 117.4 (3) | N11'—C11'—C12' | 99.8 (2) |
N1'—C1'—C2' | 100.8 (2) | C19—C11'—H11' | 109.0 |
C9—C1'—H1' | 108.8 | N11'—C11'—H11' | 109.0 |
N1'—C1'—H1' | 108.8 | C12'—C11'—H11' | 109.0 |
C2'—C1'—H1' | 108.8 | O12'—C12'—C13' | 110.1 (2) |
O2'—C2'—C3' | 111.5 (3) | O12'—C12'—C11' | 115.6 (2) |
O2'—C2'—C1' | 112.6 (2) | C13'—C12'—C11' | 102.7 (2) |
C3'—C2'—C1' | 102.3 (2) | O12'—C12'—H12' | 109.4 |
O2'—C2'—H2' | 110.1 | C13'—C12'—H12' | 109.4 |
C3'—C2'—H2' | 110.1 | C11'—C12'—H12' | 109.4 |
C1'—C2'—H2' | 110.1 | O13'—C13'—C12' | 111.7 (3) |
O3'—C3'—C2' | 110.8 (2) | O13'—C13'—C14' | 106.9 (2) |
O3'—C3'—C4' | 106.4 (2) | C12'—C13'—C14' | 103.8 (2) |
C2'—C3'—C4' | 104.5 (3) | O13'—C13'—H13' | 111.4 |
O3'—C3'—H3' | 111.6 | C12'—C13'—H13' | 111.4 |
C2'—C3'—H3' | 111.6 | C14'—C13'—H13' | 111.4 |
C4'—C3'—H3' | 111.6 | C15'—C14'—N11' | 108.5 (2) |
C5'—C4'—C3' | 114.8 (2) | C15'—C14'—C13' | 115.3 (2) |
C5'—C4'—N1' | 109.4 (2) | N11'—C14'—C13' | 104.5 (2) |
C3'—C4'—N1' | 104.0 (2) | C15'—C14'—H14' | 109.5 |
C5'—C4'—H4' | 109.5 | N11'—C14'—H14' | 109.5 |
C3'—C4'—H4' | 109.5 | C13'—C14'—H14' | 109.5 |
N1'—C4'—H4' | 109.5 | C14'—C15'—S2 | 113.4 (2) |
C4'—C5'—S1 | 111.8 (2) | C14'—C15'—H15A | 108.9 |
C4'—C5'—H5A' | 109.3 | S2—C15'—H15A | 108.9 |
S1—C5'—H5A' | 109.3 | C14'—C15'—H15B | 108.9 |
C4'—C5'—H5B' | 109.3 | S2—C15'—H15B | 108.9 |
S1—C5'—H5B' | 109.3 | H15A—C15'—H15B | 107.7 |
H5A'—C5'—H5B' | 107.9 | S2—C16'—H16A | 109.5 |
S1—C6'—H6A' | 109.5 | S2—C16'—H16B | 109.5 |
S1—C6'—H6B' | 109.5 | H16A—C16'—H16B | 109.5 |
H6A'—C6'—H6B' | 109.5 | S2—C16'—H16C | 109.5 |
S1—C6'—H6C' | 109.5 | H16A—C16'—H16C | 109.5 |
H6A'—C6'—H6C' | 109.5 | H16B—C16'—H16C | 109.5 |
H6B'—C6'—H6C' | 109.5 | N11—C12—N13 | 125.0 (3) |
N1—C2—N3 | 125.4 (3) | N11—C12—H12 | 117.5 |
N1—C2—H2 | 117.3 | N13—C12—H12 | 117.5 |
N3—C2—H2 | 117.3 | N13—C14—C15 | 118.0 (3) |
N3—C4—C5 | 118.5 (3) | N13—C14—C19 | 132.9 (3) |
N3—C4—C9 | 132.2 (3) | C15—C14—C19 | 109.1 (3) |
C5—C4—C9 | 109.2 (3) | N17—C15—C14 | 107.1 (2) |
N7—C5—C4 | 106.8 (2) | N17—C15—C16 | 131.9 (3) |
N7—C5—C6 | 132.5 (3) | C14—C15—C16 | 120.9 (3) |
C4—C5—C6 | 120.6 (3) | N16—C16—N11 | 118.5 (3) |
N6—C6—N1 | 118.2 (3) | N16—C16—C15 | 123.6 (3) |
N6—C6—C5 | 123.7 (3) | N11—C16—C15 | 117.9 (3) |
N1—C6—C5 | 118.1 (3) | N17—C18—C19 | 110.2 (2) |
N7—C8—C9 | 110.5 (3) | N17—C18—H18 | 124.9 |
N7—C8—H8 | 124.7 | C19—C18—H18 | 124.9 |
C9—C8—H8 | 124.7 | C18—C19—C14 | 104.8 (2) |
C8—C9—C4 | 104.5 (3) | C18—C19—C11' | 127.8 (3) |
C8—C9—C1' | 127.5 (3) | C14—C19—C11' | 127.3 (2) |
C4—C9—C1' | 128.0 (3) | H1WA—O1W—H2WA | 109 (3) |
C16'—S2—C15' | 100.49 (15) | | |
| | | |
C4'—N1'—C1'—C9 | −155.7 (2) | C14'—N11'—C11'—C19 | −160.9 (2) |
C4'—N1'—C1'—C2' | −30.2 (3) | C14'—N11'—C11'—C12' | −35.8 (3) |
C9—C1'—C2'—O2' | −74.6 (3) | C19—C11'—C12'—O12' | −72.8 (4) |
N1'—C1'—C2'—O2' | 163.8 (2) | N11'—C11'—C12'—O12' | 166.0 (2) |
C9—C1'—C2'—C3' | 165.6 (3) | C19—C11'—C12'—C13' | 167.3 (3) |
N1'—C1'—C2'—C3' | 44.0 (3) | N11'—C11'—C12'—C13' | 46.1 (3) |
O2'—C2'—C3'—O3' | −48.5 (3) | O12'—C12'—C13'—O13' | −48.7 (3) |
C1'—C2'—C3'—O3' | 72.1 (3) | C11'—C12'—C13'—O13' | 75.0 (3) |
O2'—C2'—C3'—C4' | −162.7 (2) | O12'—C12'—C13'—C14' | −163.5 (2) |
C1'—C2'—C3'—C4' | −42.2 (3) | C11'—C12'—C13'—C14' | −39.8 (3) |
O3'—C3'—C4'—C5' | 146.1 (2) | C11'—N11'—C14'—C15' | 135.4 (2) |
C2'—C3'—C4'—C5' | −96.7 (3) | C11'—N11'—C14'—C13' | 11.9 (3) |
O3'—C3'—C4'—N1' | −94.4 (3) | O13'—C13'—C14'—C15' | 140.0 (2) |
C2'—C3'—C4'—N1' | 22.9 (3) | C12'—C13'—C14'—C15' | −101.8 (3) |
C1'—N1'—C4'—C5' | 128.2 (3) | O13'—C13'—C14'—N11' | −101.1 (3) |
C1'—N1'—C4'—C3' | 5.1 (3) | C12'—C13'—C14'—N11' | 17.1 (3) |
C3'—C4'—C5'—S1 | −68.5 (3) | N11'—C14'—C15'—S2 | 176.47 (19) |
N1'—C4'—C5'—S1 | 175.00 (19) | C13'—C14'—C15'—S2 | −66.8 (3) |
C6'—S1—C5'—C4' | −84.8 (3) | C16'—S2—C15'—C14' | −61.1 (3) |
C6—N1—C2—N3 | 1.8 (5) | C16—N11—C12—N13 | 1.7 (5) |
C4—N3—C2—N1 | 2.4 (5) | C14—N13—C12—N11 | −1.4 (5) |
C2—N3—C4—C5 | −2.8 (4) | C12—N13—C14—C15 | −1.1 (4) |
C2—N3—C4—C9 | 177.9 (3) | C12—N13—C14—C19 | 179.0 (3) |
C8—N7—C5—C4 | −1.5 (3) | C18—N17—C15—C14 | −0.8 (3) |
C8—N7—C5—C6 | −178.0 (3) | C18—N17—C15—C16 | 176.5 (3) |
N3—C4—C5—N7 | −177.7 (3) | N13—C14—C15—N17 | −178.9 (3) |
C9—C4—C5—N7 | 1.7 (3) | C19—C14—C15—N17 | 1.0 (3) |
N3—C4—C5—C6 | −0.7 (4) | N13—C14—C15—C16 | 3.3 (4) |
C9—C4—C5—C6 | 178.7 (3) | C19—C14—C15—C16 | −176.8 (3) |
C2—N1—C6—N6 | 175.6 (3) | C12—N11—C16—N16 | 179.2 (3) |
C2—N1—C6—C5 | −5.2 (4) | C12—N11—C16—C15 | 0.6 (4) |
N7—C5—C6—N6 | 0.0 (6) | N17—C15—C16—N16 | 1.3 (6) |
C4—C5—C6—N6 | −176.1 (3) | C14—C15—C16—N16 | 178.4 (3) |
N7—C5—C6—N1 | −179.1 (3) | N17—C15—C16—N11 | 179.8 (3) |
C4—C5—C6—N1 | 4.7 (5) | C14—C15—C16—N11 | −3.1 (4) |
C5—N7—C8—C9 | 0.7 (4) | C15—N17—C18—C19 | 0.4 (4) |
N7—C8—C9—C4 | 0.3 (4) | N17—C18—C19—C14 | 0.2 (4) |
N7—C8—C9—C1' | −178.5 (3) | N17—C18—C19—C11' | −176.6 (3) |
N3—C4—C9—C8 | 178.1 (3) | N13—C14—C19—C18 | 179.2 (3) |
C5—C4—C9—C8 | −1.2 (4) | C15—C14—C19—C18 | −0.7 (3) |
N3—C4—C9—C1' | −3.2 (6) | N13—C14—C19—C11' | −4.0 (6) |
C5—C4—C9—C1' | 177.5 (3) | C15—C14—C19—C11' | 176.1 (3) |
N1'—C1'—C9—C8 | 88.6 (4) | N11'—C11'—C19—C18 | 88.6 (4) |
C2'—C1'—C9—C8 | −27.1 (5) | C12'—C11'—C19—C18 | −26.0 (5) |
N1'—C1'—C9—C4 | −89.8 (4) | N11'—C11'—C19—C14 | −87.5 (4) |
C2'—C1'—C9—C4 | 154.4 (3) | C12'—C11'—C19—C14 | 157.9 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2′—H2O′···Cl1i | 0.84 | 2.27 | 3.082 (2) | 163 |
O3′—H3O′···O1Wii | 0.84 | 1.93 | 2.724 (4) | 158 |
N1′—H1N′···Cl1iii | 0.89 (3) | 2.32 (3) | 3.199 (3) | 169 (3) |
N3—H3N···Cl4 | 0.85 (3) | 2.31 (3) | 3.097 (3) | 154 (3) |
N1′—H2N′···Cl3 | 0.84 (3) | 2.29 (3) | 3.120 (3) | 171 (3) |
N6—H6A···Cl4i | 0.83 (3) | 2.62 (3) | 3.223 (3) | 131 (2) |
N6—H6B···Cl2iii | 0.84 (3) | 2.38 (3) | 3.196 (3) | 165 (3) |
N7—H7N···Cl2iii | 0.83 (3) | 2.42 (3) | 3.232 (3) | 170 (3) |
O1W—H1WA···N1iv | 0.96 (3) | 1.87 (4) | 2.804 (4) | 162 (3) |
O1W—H2WA···Cl3 | 0.80 (4) | 2.35 (4) | 3.143 (3) | 173 (3) |
N11′—H11A···Cl2 | 0.92 (3) | 2.35 (3) | 3.268 (3) | 171 (3) |
N11′—H11B···Cl3 | 0.89 (3) | 2.34 (3) | 3.146 (3) | 151 (3) |
O12′—H12O···Cl2ii | 0.84 | 2.34 | 3.145 (2) | 162 |
N13—H13N···Cl4 | 0.87 (3) | 2.48 (3) | 3.228 (3) | 145 (3) |
O13′—H13O···S2ii | 0.84 | 2.57 | 3.364 (2) | 157 |
N17—H17N···Cl1 | 0.84 (3) | 2.39 (3) | 3.197 (3) | 163 (3) |
N16—H61A···Cl1 | 0.85 (3) | 2.51 (3) | 3.351 (3) | 171 (3) |
N16—H61B···Cl3iv | 0.82 (3) | 2.62 (3) | 3.311 (3) | 143 (3) |
C2—H2···O13′ | 0.95 | 2.46 | 3.383 (4) | 164 |
Symmetry codes: (i) −x+2, y+1/2, −z+1/2; (ii) x+1, y, z; (iii) −x+1, y+1/2, −z+1/2; (iv) −x+1, y−1/2, −z+1/2. |
Experimental details
Crystal data |
Chemical formula | 2C12H19N5O2S2+·4Cl−·H2O |
Mr | 754.58 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 100 |
a, b, c (Å) | 7.0080 (14), 18.717 (4), 24.825 (5) |
V (Å3) | 3256.3 (11) |
Z | 4 |
Radiation type | Synchrotron, λ = 0.92014 Å |
µ (mm−1) | 1.05 |
Crystal size (mm) | 0.23 × 0.20 × 0.15 |
|
Data collection |
Diffractometer | ADSC Quantum CCD Detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3864, 3864, 3821 |
Rint | 0.000 |
θmax (°) | 29.6 |
(sin θ/λ)max (Å−1) | 0.537 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.027, 0.066, 1.06 |
No. of reflections | 3864 |
No. of parameters | 454 |
No. of restraints | 12 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.40, −0.24 |
Absolute structure | Flack (1983), ???? Friedel pairs |
Absolute structure parameter | −0.03 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2'—H2O'···Cl1i | 0.84 | 2.27 | 3.082 (2) | 163 |
O3'—H3O'···O1Wii | 0.84 | 1.93 | 2.724 (4) | 158 |
N1'—H1N'···Cl1iii | 0.89 (3) | 2.32 (3) | 3.199 (3) | 169 (3) |
N3—H3N···Cl4 | 0.85 (3) | 2.31 (3) | 3.097 (3) | 154 (3) |
N1'—H2N'···Cl3 | 0.84 (3) | 2.29 (3) | 3.120 (3) | 171 (3) |
N6—H6A···Cl4i | 0.83 (3) | 2.62 (3) | 3.223 (3) | 131 (2) |
N6—H6B···Cl2iii | 0.84 (3) | 2.38 (3) | 3.196 (3) | 165 (3) |
N7—H7N···Cl2iii | 0.83 (3) | 2.42 (3) | 3.232 (3) | 170 (3) |
O1W—H1WA···N1iv | 0.96 (3) | 1.87 (4) | 2.804 (4) | 162 (3) |
O1W—H2WA···Cl3 | 0.80 (4) | 2.35 (4) | 3.143 (3) | 173 (3) |
N11'—H11A···Cl2 | 0.92 (3) | 2.35 (3) | 3.268 (3) | 171 (3) |
N11'—H11B···Cl3 | 0.89 (3) | 2.34 (3) | 3.146 (3) | 151 (3) |
O12'—H12O···Cl2ii | 0.84 | 2.34 | 3.145 (2) | 162 |
N13—H13N···Cl4 | 0.87 (3) | 2.48 (3) | 3.228 (3) | 145 (3) |
O13'—H13O···S2ii | 0.84 | 2.57 | 3.364 (2) | 157 |
N17—H17N···Cl1 | 0.84 (3) | 2.39 (3) | 3.197 (3) | 163 (3) |
N16—H61A···Cl1 | 0.85 (3) | 2.51 (3) | 3.351 (3) | 171 (3) |
N16—H61B···Cl3iv | 0.82 (3) | 2.62 (3) | 3.311 (3) | 143 (3) |
C2—H2···O13' | 0.95 | 2.46 | 3.383 (4) | 164 |
Symmetry codes: (i) −x+2, y+1/2, −z+1/2; (ii) x+1, y, z; (iii) −x+1, y+1/2, −z+1/2; (iv) −x+1, y−1/2, −z+1/2. |
Comparison of parameters between the two molecules in (I), ligand A in
1K27 and docked models (see Comment) topParametera | Molecule 1 | Molecule 2 | Ligand A in 1K27b | NeMo1c | DiMo1d |
N1'—C1'—C9—C8 | 88.6 (4) | 88.7 (4) | -54 | -56.2 | -61.1 |
C2'—C1'—C9—C4 | 154.4 (3) | 157.9 (3) | 11 | -0.1 | -7.1 |
N1'—C1'—C2'—C3' | 44.0 (3) | 46.1 (3) | -0.4 | 1.8 | 1.8 |
C1'—C2'—C3'—C4' | -42.2 (3) | -39.8 (3) | -13 | -15.7 | -15.7 |
N1'—C4'—C5'—S1 | 175.0 (2) | 176.5 (2) | 50 | 53.7 | 173.7 |
C3'—C4'—C5'—S1 | -68.5 (3) | -66.8 (3) | 170 | 170.1 | -69.9 |
C4'—C5'—S1—C6' | -84.8 (3) | -61.1 (3) | 76 | 61.4 | 172.5 |
| | | | | |
Pyrrole Ringe | Env.(C2') | Twist C11'—C12' | Env.(C4') | Env.(C4') | Env.(C4') |
Envelope Δf (Å) | 0.663 (3) | na | 0.34 | 0.37 | 0.37 |
Q(2) (Å) | 0.442 (3) | 0.453 (3) | 0.22 | 0.23 | 0.23 |
ϕ(2) (°) | 66.1 (4) | 58.0 (4) | 144 | 136 | 136 |
| | | | | |
Relative energyg | -256 | -250 | 62 | 0 | 0 |
Notes: (a) angles in °; (b) Ligand A, as the generated dication (see
Comment); (c) NeMo1: docked neutral molecule 1 (without the N3 and one
N1' H atoms); (d) DiMo1: docked from molecule 1 start, in dication form; (e)
Env.(Cn) = Envelope with flap atom Cn; (f) Δ from four-atom
envelope plane; (g) relative energy in kJ mol-1 for DFT-optimized coordinates
from starting models above (see Comment). |
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The title compound, (I), a potent inhibitor of methylthioadenosine phosphorylase (MTAP), was prepared by Evans et al. (2004) as part of a synthesis program aimed at anticancer lead compounds. The structure and stereochemistry were established prior to its subsequent definition in the active site of the enzyme [Protein Data Bank (PDB) ID code 1K27 used hereafter), as reported by Singh et al. (2004). This report notes the details of the crystal structure of the double-protonated (dication) chloride salt, which includes a water of crystallization, (I). Additional information about the computational docking of the compound in the enzyme using the 1K27 coordinates has been determined using the docking program GOLD (Jones et al., 1997; Nissink et al., 2002). The results are discussed in the light of the different molecular conformations found for the two independent molecules as compared with that observed bound in the MTAP enzyme structure and the relative energies calculated by DFT (density functional theory) methods (ADF2009.01, 2009).
The structure contains two independent dicationic C12H19N5O2S molecules, four chloride anions and one water molecule of crystallization. These two molecule conformations (molecules 1 and 2 hereafter) have atom labels related by the numerical addition of 10 (e.g. N3 and N13, see Fig. 1).
The crystal packing can be described as a one-dimensional array built along the b screw axis, with some links along the c axis, utilizing a network of hydrogen bonds: N—H···Cl, (C)O—H···Cl, O(water)—H···Cl, O(water)—H···N and one O—H···S (Table 1, Fig. 2). There are no strong links between the lattices, with the methylthio (e.g. C6', S1, C5') interactions defining the spacing up the a cell axes. The basic building blocks consist of D11(2) moiety types (Bernstein et al., 1995) which build to larger D22 forms mainly; there are only a few examples of other types e.g. bifurcated binding which generate the R12(7) (entries 7 and 8, Table 1) and R12(8) (entries 5 and 10, Table 1) motifs. The key hydrogen bonds that promote the observed conformations in both molecules, as distinct from that found in the enzyme (Table 2), involve the additional H atoms that give the overall 2+ charge (namely on atoms N3, N13, N1' and N11'). These latter atoms form inter-linking bonds (see entries 4 and 14, and 5 and 12 in Table 1) as shown in Fig. 3 which could not form if the conformations were as found in the enzyme.
It is common practice to take X-ray-diffraction-derived molecular parameters as starting models for ligand docking studies. In this case it was of some interest to determine if the docking computations using the software package GOLD could rotate the two rings ~130° about the C1'—C9 bond to reproduce the observed conformation in the enzyme (see Table 2, Fig. 4). The initial test starting with the found 1K27 ligand coordinates (`ligand A': with H atoms in calculated positions) without using any constraints was successful. By contrast, neither the dication nor the neutral molecule based on molecules 1 and 2 gave any correctly docked solutions. Only when the pyrrolidine ring was allowed to flex, using the flip ring corners option, did any correct solutions appear: both the dication-based coordinates and the `ligand A' sets gave some good matches but not with the highest docking scores.
To obtain the closest matches with the observed ligand A in 1K27, coupled with the highest docking scores for all the models, required three constraints: specifying which enzyme atoms had hydrogen bonds (but not which ligand atoms were involved), flipping the pyramidal N atom in the pyrrolidine ring and exploring the ring conformations. Using GOLD's CHEMSCORE and CHEMPLP scoring regimes gave the highest numerical score for the (starting coordinate) `ligand A' set, the neutral and dication (molecule 1)-based coordinates scoring somewhat less, but correctly in terms of matching the ligand conformation and position in 1K27. There was some variation in final positioning of the terminal S-methyl group in the dication run (Table 2, DiMo1 column) as indicated in Fig. 5 and Table 2.
These results led us to calculate the molecular energies using DFT methods (ADF2009.01, 2009). The BLYP functional formed from the combination of the local density approximation (LDA) parameterization by Vosko et al. (1980), VWN5, with the B88 exchange gradient correction (Becke, 1988) and the LYP correlation gradient correction (Lee et al., 1988) were used. The basis set used was triple-zeta quality for all valence orbitals and included two sets of polarization functions on each atom (Van Lenthe & Baerends, 2003). The polarization functions are '1p1d' on the H atoms and '1 d1f' on the C, N and O atoms. The positions of the heavy atoms were frozen at the values taken from the crystal or docked structures but the coordinates of the H atoms were allowed to relax. The energy differences found, from the specified starting models, relative to the docked conformation are shown in Table 2 (final DFT calculated geometries are not given).
The similarity of results for the molecule 1 and 2 conformations in geometry and energy [difference 6 kJ mol-1 (1.24 kcal mol-1)] gives credence to the calculations, which show that the enzyme-bound `ligand A' dication conformation has much higher energy (~253 kJ mol-1). The energy required to distort the molecule to its docking geometry must be made up by energy gained through favorable interactions with the enzyme. A phosphate species is well placed to strongly interact with the cation. Furthermore, the protein structure and docking studies suggest that when in place the cation will form several hydrogen bonds with its host: four such P—O···H—O,N interactions are observed. Together, these bonds should be able to stabilize the cation in its docked conformation. In the case of the neutral molecule, the docked conformation is found to be lower in energy by 62 kJ mol-1 than the conformation suggested by the 1K27 ligand A crystal structure.
These latter results strongly suggest that docking of the free ligand molecules 1 and 2 in the 1K27 enzyme (and by analogy for other similar cases) must include hydrogen-bonding interactions. This was also indicated by the final (successful) criteria applied in the GOLD docking runs. A sobering corollary to this finding is that crystallographically determined free ligand conformations may not be reproduced in enzyme binding sites, which may limit their potential as starting models for drug discovery.