Ethyl 2-[N-(tert-butyl­oxy­carbonyl)-L-alanyl­amino]-4-methyl-1,3-thia­zole-5-carboxyl­ate reveals a trans orientation of the preceding amide N-H with respect to the thia­zole-ring sulfur

The title mol­ecule, C₁₅H₂₃N₃O₅S, was prepared as a synthetic precursor to 4-methyl­thia­zole-based DNA minor groove binders which would bear chiral amino acids in the sequence. The crystallographic evidence presented herein shows that the aromatic amide NH group preceding the thia­zole ring points away from the direction of sulfur. The mol­ecule is biplanar, with the dihedral angle between the N-terminus peptide moiety and the thia­zole-containing plane being 49.7 (5)°, with a bend at the C[alpha] carbon.

S1. Comment

One approach to the general problem of developing DNA sequence-specific reagents is by modifying the lead compounds based on the principles of DNA recognition. Distamycin (Dst) and Netropsin (Nt) are DNA binding compounds that bind in the minor groove of AT rich sequences of DNA. The determinants in the DNA recognition of these molecules were deciphered from the crystal structures of free Nt (Berman et al., 1979) and also that of the complexes of Nt (Kopka et al., 1985) and Dst (Coli et al., 1987) with the respective target DNA sequences. The sequence-specificity in the binding of these molecules is a result of the hydrogen-bonding interactions between the amide NH groups and the adenine N3 or thymine O2 atoms, and the close van der Waals contact between the C3(H) of the pyrrole residues and thymine –CH₃ groups. Replacement of pyrrole by other heterocyclic moieties capable of specific DNA recognition by hydrogen-bond acceptance, such as imidazole, pyridine or oxazole led to the generation of molecules that recognize GC rich sequences of DNA and are termed `lexitropsins' or information reading molecules (for recent reviews see: Wemmer & Dervan, 1997; Baily & Chaires, 1998).

Thiazole lexitropsins with amino and carboxy substituents at 2- and 5- positions, respectively, along with alkyl substitution at position 4- (type II thiazole lexitropsins) are expected to be more discriminating than the parent antibiotics Dst and Nt against GC tolerance (Rao et al., 1990), as this substitution pattern favours orientation of S towards the minor groove of DNA.

Yet another important component of molecular recognition is ligand chirality and one way of modulating the sequence specificity and affinity of prototype lexitropsins is by intoducing chiral amino acids (Herman et al., 1998). As a part of our continuing effort in the development of DNA binding molecules (Bhattacharya & Thomas, 1998, 2000a, 2000b) we synthesized the title compound, (I), a dipeptide precursor in the synthesis of type II thiazole containing lexitropsins. We attempted to solve the crystal structure of this molecule to determine (a) the relative orientation of the amide unit preceding the thiazole ring with respect to the S atom, (b) the overall shape of the molecule. \sch

The title molecule (see Fig. 1) was found to be biplanar with the dihedral angle between the mean plane (A) containing N terminus peptide moeity, (C3—C4—O1—C0'-N1—C1A) and the mean plane (B) containing the thiazole ring, (C1'-N2—C5—N3—C6—C7—S1—C8'-O9—C10) being 49.7 (5)° with a bend at the Cα carbon·The maximum deviation of the atoms defining the two planes is 0.100 (4) and 0.040 (4) Å for planes (A) and (B), respectively. The thiazole ring is planar, with a maximum deviation of the ring atoms from the plane being 0.005 (4) Å. Within the ring, the bonding angle at S1, (C5—S1—C7) is 88.36 (15)°, which is unusually small. The length of the C—S bonds is also on the lower side with average of 1.715 (4) Å. The carbonyl groups that are on either side of the thiazole ring lie almost in the plane of the ring [deviations 0.063 (4) and 0.039 (4) Å, respectively, for O1' and O8'], and are pointing in the same direction as sulfur. The non-bonded distances of O1' and O8' from S1 are 2.737 (4) and 2.939 (4) Å, respectively, which are significantly shorter than the sum of van der Waals radii of S and O (3.50 Å) (Bondi, 1964).

It is interesting to note that the aromatic amide N—H preceeding thiazole ring points in the direction opposite to that of the sulfur atom. As mentioned earlier, minor groove binding of type II thiazole containing lexitropsins would require the preceeding amide N—H to be pointed in the same direction as that of the sulfur atom. It is worthwhile to note at this point that in the NMR structure of a thiazole/pyrrole lexitropsin complexed with a dodecanucleotide (Kumar et al., 1990), the N-terminus thiazole unit was found to be binding in intercalative fashion rather than minor groove binding. This unusual observation could be explained in the light of the present structure. In the absence of the preceding amide –NH pointing towards the minor groove, the planar aromatic ring of thiazole containing lexitropsins could act as an intercalating chromophore, as observed in the case mentioned above. Thus the results of the observations emerging from the present structure should help the future design of thiazole based DNA binding compounds.

S2. Experimental

The synthesis of the title compound was carried out by coupling of the t-Boc -alanine with ethyl 4-methyl-2-aminothiazole-5-carboxylate in the presence of dicyclohexyl carbodiimide and hydroxybenzotriazole. The pure compound was isolated in 96% yield upon coloumn chromatography over silica gel using 20–30% petrolium ether/ethyl acetate as eluent. The diffraction quality crystals were obtained by layering acetone solution of (I) (300 µl, 50 mM) over 5 ml of water in a test tube. ¹H NMR: 200 MHz (CDCl₃, δ p.p.m.), 1.36 (t, 3H), 1.45 (s, 9H), 1.5 (3H merging with the Boc peak), 2.57 (s, 3H), 4.29 (q, 2H), 4.55 (bs, 1H), 5.47 (bs, 1H), 10.64 (bs, 1H). IR: (Nujol, ν, cm⁻¹) 3269, 1707, 1667, 1527.

S3. Refinement

Molecule (I) crystallized in the monoclinic system; space group C2, Cm or C2/m from systematic absences; C2 was chosen and confirmed by the analysis. H atoms were treated as riding atoms (C—H₃ 0.96, C—H₂ 0.97,C—H 0.98, N—H 0.86). The distance between C10 and C11 was fixed at 1.500 (3) Å to avoid the shortening due to thermal vibration.

Computing details

Data collection: CAD-4 Software (Enraf-Nonius, 1989); cell refinement: CAD-4 Software; data reduction: MolEN (Fair, 1990); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1990) and ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: PLATON and SHELXL97.

Figures

Fig. 1. View of the title compound with the atom-numbering scheme. Displacement ellipsoids for non-H atoms are drawn at the 50% probability level.

Ethyl 2-[N-(tert-butyloxycarbonyl)-L-alanylamino]-4-methyl-1,3-thiazole-5 -carboxylate

Crystal data

C15H23N3O5S	F(000) = 760
Mr = 357.42	Dx = 1.265 Mg m^−3
Monoclinic, C2	Cu Kα radiation, λ = 1.54180 Å
a = 19.2711 (10) Å	Cell parameters from 25 reflections
b = 9.769 (3) Å	θ = 10–35°
c = 10.2592 (10) Å	µ = 1.78 mm^−1
β = 103.666 (13)°	T = 293 K
V = 1876.8 (6) Å^3	Plate, colourless
Z = 4	0.13 × 0.06 × 0.04 mm

Data collection

ENRAF-NONIUS CAD-4 diffractometer	1756 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.021
Graphite monochromator	θmax = 69.9°, θmin = 4.4°
ω/2θ scans	h = 0→23
Absorption correction: ψ scan (North et al., 1968)	k = 0→11
Tmin = 0.738, Tmax = 0.931	l = −12→12
1944 measured reflections	2 standard reflections every 60 min
1886 independent reflections	intensity decay: <2.0%

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.038	w = 1/[σ^2(Fo^2) + (0.074P)^2 + 0.4897P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.109	(Δ/σ)max = 0.018
S = 1.04	Δρmax = 0.34 e Å^−3
1886 reflections	Δρmin = −0.18 e Å^−3
207 parameters	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
2 restraints	Extinction coefficient: 0.0027 (3)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack,(1983)
Secondary atom site location: difference Fourier map	Absolute structure parameter: −0.03 (2)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
C1	0.2714 (3)	0.8387 (14)	−0.1010 (5)	0.160 (4)
H1A	0.2662	0.7496	−0.0650	0.240*
H1B	0.2752	0.8300	−0.1922	0.240*
H1C	0.2305	0.8937	−0.0980	0.240*
C2	0.4031 (3)	0.8156 (7)	0.0015 (5)	0.1119 (19)
H2A	0.4424	0.8569	0.0644	0.168*
H2B	0.4157	0.8030	−0.0829	0.168*
H2C	0.3924	0.7284	0.0353	0.168*
C3	0.35335 (17)	1.04047 (13)	−0.07835 (15)	0.119 (2)
H3A	0.3111	1.0960	−0.0956	0.179*
H3B	0.3670	1.0235	−0.1610	0.179*
H3C	0.3913	1.0874	−0.0173	0.179*
C4	0.33876 (17)	0.90706 (13)	−0.01775 (15)	0.0731 (10)
O1	0.32967 (6)	0.94856 (12)	0.11453 (11)	0.0680 (6)
C0'	0.31757 (7)	0.85388 (13)	0.20182 (11)	0.0585 (7)
O0'	0.30309 (6)	0.73517 (12)	0.17723 (12)	0.0901 (9)
N1	0.32382 (7)	0.91199 (13)	0.32228 (11)	0.0641 (7)
H1	0.3326	0.9982	0.3320	0.077*
C1A	0.31590 (7)	0.83149 (13)	0.43640 (11)	0.0581 (7)
H1AA	0.3079	0.7356	0.4089	0.070*
C1B	0.3822 (2)	0.8409 (6)	0.5504 (4)	0.0861 (12)
H1B1	0.4224	0.8042	0.5216	0.129*
H1B2	0.3750	0.7894	0.6258	0.129*
H1B3	0.3913	0.9349	0.5760	0.129*
C1'	0.25284 (19)	0.8821 (3)	0.4848 (3)	0.0509 (7)
O1'	0.23896 (15)	1.0042 (2)	0.4951 (3)	0.0661 (6)
N2	0.21172 (13)	0.7829 (3)	0.5221 (2)	0.0511 (5)
H2	0.2228	0.6991	0.5113	0.061*
C5	0.15358 (15)	0.8067 (3)	0.5757 (3)	0.0475 (6)
N3	0.11963 (14)	0.7040 (3)	0.6120 (3)	0.0542 (6)
C6	0.06421 (17)	0.7486 (4)	0.6642 (3)	0.0559 (7)
C6'	0.0186 (2)	0.6434 (4)	0.7081 (5)	0.0801 (11)
H6'1	0.0393	0.5545	0.7051	0.120*
H6'2	−0.0283	0.6452	0.6494	0.120*
H6'3	0.0152	0.6628	0.7982	0.120*
C7	0.05840 (17)	0.8894 (3)	0.6674 (3)	0.0551 (7)
S1	0.12288 (4)	0.96626 (6)	0.60170 (8)	0.0570 (2)
C8'	0.00871 (18)	0.9806 (5)	0.7128 (4)	0.0671 (8)
O8'	0.01048 (17)	1.1029 (3)	0.7036 (4)	0.0948 (10)
O9	−0.03728 (16)	0.9129 (3)	0.7656 (3)	0.0872 (8)
C10	−0.0873 (3)	1.0027 (6)	0.8134 (6)	0.1105 (17)
H10A	−0.1214	1.0432	0.7385	0.133*
H10B	−0.0618	1.0754	0.8692	0.133*
C11	−0.1240 (4)	0.9120 (7)	0.8925 (9)	0.157 (3)
H11A	−0.1486	0.8404	0.8358	0.235*
H11B	−0.1577	0.9645	0.9271	0.235*
H11C	−0.0893	0.8724	0.9657	0.235*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.117 (4)	0.284 (12)	0.070 (3)	−0.029 (6)	0.002 (2)	−0.020 (5)
C2	0.143 (4)	0.108 (4)	0.095 (3)	0.058 (4)	0.047 (3)	−0.002 (3)
C3	0.175 (5)	0.110 (4)	0.093 (3)	0.041 (4)	0.069 (4)	0.034 (3)
C4	0.082 (2)	0.083 (3)	0.0574 (17)	0.019 (2)	0.0235 (15)	0.0046 (17)
O1	0.0926 (14)	0.0556 (14)	0.0639 (11)	0.0128 (12)	0.0345 (10)	0.0073 (11)
C0'	0.0647 (16)	0.0499 (19)	0.0630 (16)	0.0007 (14)	0.0194 (13)	0.0012 (14)
O0'	0.132 (2)	0.0593 (17)	0.0757 (16)	−0.0286 (16)	0.0191 (16)	−0.0123 (14)
N1	0.101 (2)	0.0345 (13)	0.0694 (15)	−0.0052 (13)	0.0466 (14)	−0.0001 (11)
C1A	0.0784 (18)	0.0328 (13)	0.0717 (17)	−0.0004 (14)	0.0345 (14)	0.0066 (14)
C1B	0.076 (2)	0.089 (3)	0.095 (3)	0.014 (2)	0.0232 (18)	0.025 (3)
C1'	0.0704 (18)	0.0304 (15)	0.0561 (15)	−0.0016 (11)	0.0236 (13)	0.0004 (11)
O1'	0.0869 (15)	0.0273 (12)	0.0958 (15)	−0.0012 (9)	0.0450 (13)	0.0027 (10)
N2	0.0693 (14)	0.0275 (10)	0.0622 (13)	−0.0019 (10)	0.0270 (11)	0.0000 (10)
C5	0.0631 (15)	0.0298 (13)	0.0502 (12)	−0.0023 (11)	0.0149 (11)	0.0006 (10)
N3	0.0690 (15)	0.0308 (12)	0.0674 (14)	−0.0022 (10)	0.0251 (12)	0.0010 (10)
C6	0.0595 (16)	0.0424 (15)	0.0680 (17)	−0.0007 (13)	0.0194 (13)	0.0026 (13)
C6'	0.086 (2)	0.055 (2)	0.112 (3)	−0.0030 (19)	0.047 (2)	0.010 (2)
C7	0.0591 (17)	0.0458 (17)	0.0608 (16)	0.0043 (13)	0.0147 (13)	−0.0011 (14)
S1	0.0666 (4)	0.0318 (4)	0.0743 (5)	0.0025 (3)	0.0201 (3)	−0.0004 (3)
C8'	0.0628 (17)	0.056 (2)	0.082 (2)	0.0035 (17)	0.0156 (15)	−0.0074 (18)
O8'	0.0875 (18)	0.0509 (16)	0.149 (3)	0.0145 (13)	0.0331 (18)	−0.0126 (17)
O9	0.0866 (17)	0.0715 (19)	0.117 (2)	0.0099 (14)	0.0518 (15)	−0.0043 (16)
C10	0.106 (3)	0.096 (4)	0.148 (4)	0.019 (3)	0.066 (3)	−0.015 (3)
C11	0.150 (6)	0.113 (6)	0.252 (9)	0.004 (4)	0.135 (7)	−0.005 (6)

Geometric parameters (Å, º)

C1—C4	1.529 (7)	N2—C5	1.380 (4)
C2—C4	1.504 (5)	C5—N3	1.299 (4)
C3—C4	1.499 (2)	C5—S1	1.710 (3)
C4—O1	1.466 (2)	N3—C6	1.374 (4)
O1—C0'	1.346 (2)	C6—C7	1.381 (5)
C0'—O0'	1.206 (2)	C6—C6'	1.490 (5)
C0'—N1	1.339 (2)	C7—C8'	1.463 (5)
N1—C1A	1.448 (2)	C7—S1	1.720 (3)
C1A—C1'	1.501 (4)	C8'—O8'	1.199 (6)
C1A—C1B	1.518 (4)	C8'—O9	1.320 (5)
C1'—O1'	1.233 (4)	O9—C10	1.470 (5)
C1'—N2	1.362 (4)	C10—C11	1.489 (3)
O1—C4—C2	108.5 (2)	C1'—N2—C5	125.0 (3)
O1—C4—C3	102.6 (1)	N3—C5—N2	119.7 (3)
C2—C4—C3	110.0 (3)	N3—C5—S1	116.3 (2)
O1—C4—C1	111.5 (3)	N2—C5—S1	124.0 (2)
C2—C4—C1	112.3 (5)	C5—N3—C6	110.9 (3)
C3—C4—C1	111.5 (4)	N3—C6—C7	113.6 (3)
C0'—O1—C4	120.2 (1)	N3—C6—C6'	117.9 (3)
O0'—C0'—N1	124.5 (1)	C7—C6—C6'	128.5 (3)
O0'—C0'—O1	126.2 (1)	C6—C7—C8'	132.6 (3)
N1—C0'—O1	109.3 (1)	C6—C7—S1	110.8 (3)
C0'—N1—C1A	120.8 (1)	C8'—C7—S1	116.5 (3)
N1—C1A—C1'	109.71 (12)	C5—S1—C7	88.36 (15)
N1—C1A—C1B	111.09 (18)	O8'—C8'—O9	124.4 (4)
C1'—C1A—C1B	109.0 (2)	O8'—C8'—C7	123.3 (4)
O1'—C1'—N2	120.8 (3)	O9—C8'—C7	112.3 (4)
O1'—C1'—C1A	123.8 (3)	C8'—O9—C10	113.2 (4)
N2—C1'—C1A	115.4 (2)	O9—C10—C11	105.1 (4)
C2—C4—O1—C0'	−61.7 (3)	S1—C5—N3—C6	0.5 (3)
C3—C4—O1—C0'	−178.1 (1)	C5—N3—C6—C7	−0.8 (4)
C1—C4—O1—C0'	62.5 (5)	C5—N3—C6—C6'	178.7 (3)
C4—O1—C0'—O0'	−11.18 (15)	N3—C6—C7—C8'	179.8 (3)
C4—O1—C0'—N1	169.05 (15)	C6'—C6—C7—C8'	0.4 (7)
O0'—C0'—N1—C1A	2.4 (2)	N3—C6—C7—S1	0.8 (4)
O1—C0'—N1—C1A	−177.8 (1)	C6'—C6—C7—S1	−178.6 (3)
C0'—N1—C1A—C1'	−117.15 (14)	N3—C5—S1—C7	0.0 (2)
C0'—N1—C1A—C1B	122.3 (2)	N2—C5—S1—C7	−178.8 (3)
N1—C1A—C1'—O1'	−42.4 (4)	C6—C7—S1—C5	−0.4 (3)
C1B—C1A—C1'—O1'	79.4 (4)	C8'—C7—S1—C5	−179.6 (3)
N1—C1A—C1'—N2	139.6 (2)	C6—C7—C8'—O8'	−177.4 (4)
C1B—C1A—C1'—N2	−98.6 (3)	S1—C7—C8'—O8'	1.5 (5)
O1'—C1'—N2—C5	−1.4 (5)	C6—C7—C8'—O9	3.1 (6)
C1A—C1'—N2—C5	176.6 (2)	S1—C7—C8'—O9	−177.9 (2)
C1'—N2—C5—N3	−177.6 (3)	O8'—C8'—O9—C10	−0.1 (6)
C1'—N2—C5—S1	1.1 (4)	C7—C8'—O9—C10	179.3 (4)
N2—C5—N3—C6	179.3 (2)	C8'—O9—C10—C11	−169.0 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N3^i	0.86	2.23	3.071 (3)	166
N2—H2···O1′^ii	0.86	2.05	2.903 (4)	173
C3—H3A···O0′^iii	0.96	2.55	3.506 (3)	172

Symmetry codes: (i) −x+1/2, y+1/2, −z+1; (ii) −x+1/2, y−1/2, −z+1; (iii) −x+1/2, y+1/2, −z.