Ethyl 2-[({[4-amino-5-cyano-6-(methyl-sulfan-yl)pyridin-2-yl]carbamo-yl}meth-yl)sulfan-yl]acetate monohydrate.

The title compound, C13H16N4O3S2·H2O, crystallizes in a 'folded' conformation with the ester group lying over the carbamoyl moiety, with one solvent water mol-ecule. The mol-ecular conformation is stabilized by an intra-molecular C-H⋯O hydrogen bond, and an N-H⋯O hydrogen-bonding inter-action involving the lattice water mol-ecule. The packing involves N-H⋯N, N-H⋯O, O-H⋯N and O-H⋯O hydrogen bonds and consists of tilted layers running approximately parallel to the c axis, with the ester groups on the outer sides of the layers and with channels running parallel to (101).

Related literature

For the synthesis of amino-cyano pyridines, see: Shi et al. (2005 ▶). For pyridines as inter­mediates in the synthesis of different heterocyclic compounds, see: Konda et al. (2010 ▶). For the pharmaceutical activity of functionalized pyridine derivatives, see: Dorigo et al. (1993 ▶); Dolle et al. (1995 ▶); Murata et al. (2003 ▶). For industrial applications of pyridine compounds, see: Lohray et al. (2004 ▶); Merja et al. (2004 ▶); Chaki et al. (1995 ▶); Thomae et al. (2007 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C13H16N4O3S2·H2O

M = 358.45

Triclinic,

a = 9.0806 (12) Å

b = 9.2444 (12) Å

c = 10.7856 (14) Å

α = 101.843 (2)°

β = 100.1750 (19)°

γ = 105.9480 (19)°

V = 825.48 (19) Å3

Z = 2

Mo Kα radiation

μ = 0.35 mm−1

T = 150 K

0.26 × 0.26 × 0.12 mm

Data collection

Bruker SMART APEX CCD diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2013 ▶) T min = 0.83, T max = 0.96

15313 measured reflections

4292 independent reflections

3773 reflections with I > 2σ(I)

R int = 0.034

Refinement

R[F 2 > 2σ(F 2)] = 0.037

wR(F 2) = 0.099

S = 1.05

4292 reflections

210 parameters

H-atom parameters constrained

Δρmax = 0.44 e Å−3

Δρmin = −0.37 e Å−3

Data collection: APEX2 (Bruker, 2013 ▶); cell refinement: SAINT (Bruker, 2013 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXT (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg & Putz, 2012 ▶); software used to prepare material for publication: SHELXTL (Sheldrick, 2008 ▶).

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536814012495/sj5406sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814012495/sj5406Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S1600536814012495/sj5406Isup3.cml

CCDC reference: 1005734

Additional supporting information: crystallographic information; 3D view; checkCIF report

C13H16N4O3S2·H2O	Z = 2
Mr = 358.45	F(000) = 376
Triclinic, P1	Dx = 1.442 Mg m−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 9.0806 (12) Å	Cell parameters from 9913 reflections
b = 9.2444 (12) Å	θ = 2.4–29.2°
c = 10.7856 (14) Å	µ = 0.35 mm−1
α = 101.843 (2)°	T = 150 K
β = 100.1750 (19)°	Plate, colourless
γ = 105.9480 (19)°	0.26 × 0.26 × 0.12 mm
V = 825.48 (19) Å3

Bruker SMART APEX CCD diffractometer	4292 independent reflections
Graphite monochromator	3773 reflections with I > 2σ(I)
Detector resolution: 8.3660 pixels mm-1	Rint = 0.034
φ and ω scans	θmax = 29.2°, θmin = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2013)	h = −12→12
Tmin = 0.83, Tmax = 0.96	k = −12→12
15313 measured reflections	l = −14→14

Refinement on F2	0 restraints
Least-squares matrix: full	Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.037	H-atom parameters constrained
wR(F2) = 0.099	w = 1/[σ2(Fo2) + (0.0515P)2 + 0.3031P] where P = (Fo2 + 2Fc2)/3
S = 1.05	(Δ/σ)max = 0.001
4292 reflections	Δρmax = 0.44 e Å−3
210 parameters	Δρmin = −0.37 e Å−3

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs 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.

	x	y	z	Uiso*/Ueq
S1	1.14877 (5)	0.74276 (5)	0.62470 (3)	0.0316 (1)
S2	0.40426 (4)	0.82259 (4)	0.00905 (3)	0.0218 (1)
O1	0.50975 (12)	0.88281 (13)	0.30154 (9)	0.0263 (3)
O2	0.16728 (13)	0.58384 (14)	0.15365 (11)	0.0325 (3)
O3	0.38626 (12)	0.51837 (12)	0.14447 (9)	0.0244 (3)
N1	0.91851 (13)	0.79013 (14)	0.46377 (11)	0.0200 (3)
N2	1.05234 (16)	0.87115 (18)	0.92745 (12)	0.0330 (4)
N3	0.73517 (14)	0.97498 (15)	0.76432 (11)	0.0257 (3)
N4	0.73715 (13)	0.82181 (14)	0.30697 (10)	0.0204 (3)
C1	0.98222 (15)	0.80180 (16)	0.58659 (13)	0.0193 (3)
C2	0.92486 (15)	0.86183 (16)	0.69216 (12)	0.0192 (3)
C3	0.79351 (15)	0.91523 (16)	0.66734 (12)	0.0194 (3)
C4	0.72390 (15)	0.89929 (16)	0.53540 (12)	0.0207 (4)
C5	0.79125 (15)	0.83911 (15)	0.44086 (12)	0.0185 (3)
C6	1.1786 (2)	0.6781 (3)	0.46517 (17)	0.0480 (7)
C7	0.99695 (16)	0.86718 (17)	0.82188 (13)	0.0225 (4)
C8	0.60550 (15)	0.84739 (16)	0.24588 (12)	0.0194 (3)
C9	0.59280 (16)	0.82956 (17)	0.10018 (13)	0.0215 (4)
C10	0.28999 (17)	0.61849 (17)	−0.02404 (13)	0.0247 (4)
C11	0.27024 (16)	0.57242 (17)	0.09924 (13)	0.0237 (4)
C12	0.3870 (2)	0.4842 (2)	0.27094 (15)	0.0315 (5)
C13	0.5180 (2)	0.4186 (2)	0.30413 (16)	0.0335 (5)
O4	0.91965 (12)	0.72768 (13)	0.12641 (10)	0.0287 (3)
H3A	0.79320	1.00160	0.84830	0.0310*
H3B	0.65660	1.01610	0.74450	0.0310*
H4	0.63290	0.92930	0.51240	0.0250*
H4A	0.79970	0.79450	0.25550	0.0240*
H6A	1.08460	0.59240	0.41090	0.0720*
H6B	1.27060	0.64170	0.47300	0.0720*
H6C	1.19680	0.76500	0.42460	0.0720*
H9A	0.61410	0.73250	0.06270	0.0260*
H9B	0.67560	0.91820	0.08960	0.0260*
H10A	0.18450	0.59830	−0.08140	0.0300*
H10B	0.34350	0.55330	−0.07120	0.0300*
H12A	0.28430	0.40770	0.26670	0.0380*
H12B	0.40330	0.58080	0.33910	0.0380*
H13A	0.50470	0.32690	0.23340	0.0500*
H13B	0.51520	0.38810	0.38570	0.0500*
H13C	0.61990	0.49790	0.31490	0.0500*
H4B	0.94980	0.77280	0.07090	0.0340*
H4C	0.99220	0.69030	0.14630	0.0340*

	U11	U22	U33	U12	U13	U23
S1	0.0310 (2)	0.0527 (3)	0.0213 (2)	0.0314 (2)	0.0049 (1)	0.0089 (2)
S2	0.0225 (2)	0.0265 (2)	0.0184 (2)	0.0128 (1)	0.0009 (1)	0.0072 (1)
O1	0.0212 (5)	0.0418 (6)	0.0196 (5)	0.0182 (4)	0.0036 (4)	0.0063 (4)
O2	0.0282 (5)	0.0444 (7)	0.0334 (6)	0.0193 (5)	0.0132 (5)	0.0134 (5)
O3	0.0255 (5)	0.0313 (5)	0.0225 (5)	0.0142 (4)	0.0094 (4)	0.0108 (4)
N1	0.0184 (5)	0.0261 (6)	0.0182 (5)	0.0121 (4)	0.0041 (4)	0.0054 (4)
N2	0.0328 (7)	0.0520 (9)	0.0211 (6)	0.0253 (6)	0.0055 (5)	0.0097 (6)
N3	0.0227 (6)	0.0408 (7)	0.0167 (5)	0.0186 (5)	0.0037 (4)	0.0041 (5)
N4	0.0185 (5)	0.0299 (6)	0.0156 (5)	0.0132 (5)	0.0038 (4)	0.0053 (4)
C1	0.0171 (6)	0.0242 (6)	0.0188 (6)	0.0111 (5)	0.0032 (5)	0.0055 (5)
C2	0.0168 (6)	0.0253 (6)	0.0167 (6)	0.0098 (5)	0.0024 (4)	0.0054 (5)
C3	0.0159 (6)	0.0238 (6)	0.0180 (6)	0.0075 (5)	0.0030 (4)	0.0039 (5)
C4	0.0175 (6)	0.0281 (7)	0.0179 (6)	0.0119 (5)	0.0022 (5)	0.0047 (5)
C5	0.0158 (5)	0.0225 (6)	0.0168 (6)	0.0078 (5)	0.0010 (4)	0.0046 (5)
C6	0.0526 (11)	0.0851 (15)	0.0276 (8)	0.0544 (11)	0.0149 (7)	0.0128 (9)
C7	0.0190 (6)	0.0314 (7)	0.0202 (6)	0.0135 (5)	0.0053 (5)	0.0056 (5)
C8	0.0180 (6)	0.0226 (6)	0.0178 (6)	0.0088 (5)	0.0022 (4)	0.0050 (5)
C9	0.0190 (6)	0.0309 (7)	0.0190 (6)	0.0128 (5)	0.0047 (5)	0.0097 (5)
C10	0.0264 (7)	0.0266 (7)	0.0197 (6)	0.0094 (6)	0.0026 (5)	0.0045 (5)
C11	0.0223 (6)	0.0249 (7)	0.0235 (6)	0.0087 (5)	0.0043 (5)	0.0053 (5)
C12	0.0360 (8)	0.0431 (9)	0.0269 (7)	0.0198 (7)	0.0151 (6)	0.0184 (7)
C13	0.0391 (9)	0.0396 (9)	0.0301 (8)	0.0198 (7)	0.0100 (6)	0.0161 (7)
O4	0.0258 (5)	0.0376 (6)	0.0301 (5)	0.0171 (5)	0.0113 (4)	0.0116 (5)

S1—C1	1.7550 (15)	C2—C3	1.415 (2)
S1—C6	1.7952 (18)	C2—C7	1.4208 (19)
S2—C9	1.7945 (15)	C3—C4	1.4111 (18)
S2—C10	1.8113 (16)	C4—C5	1.3776 (19)
O1—C8	1.2181 (18)	C8—C9	1.5262 (18)
O2—C11	1.2051 (19)	C10—C11	1.502 (2)
O3—C11	1.3436 (19)	C12—C13	1.499 (3)
O3—C12	1.4613 (19)	C4—H4	0.9500
O4—H4C	0.8400	C6—H6B	0.9800
O4—H4B	0.8400	C6—H6A	0.9800
N1—C1	1.3181 (18)	C6—H6C	0.9800
N1—C5	1.3543 (19)	C9—H9B	0.9900
N2—C7	1.1494 (19)	C9—H9A	0.9900
N3—C3	1.3414 (18)	C10—H10B	0.9900
N4—C5	1.4013 (16)	C10—H10A	0.9900
N4—C8	1.3639 (19)	C12—H12B	0.9900
N3—H3A	0.9100	C12—H12A	0.9900
N3—H3B	0.9100	C13—H13C	0.9800
N4—H4A	0.9100	C13—H13A	0.9800
C1—C2	1.4088 (19)	C13—H13B	0.9800
C1—S1—C6	101.26 (8)	O2—C11—C10	125.82 (14)
C9—S2—C10	101.89 (7)	O3—C12—C13	108.59 (14)
C11—O3—C12	115.32 (12)	C5—C4—H4	121.00
H4B—O4—H4C	102.00	C3—C4—H4	121.00
C1—N1—C5	116.87 (12)	S1—C6—H6A	109.00
C5—N4—C8	127.62 (12)	S1—C6—H6B	109.00
H3A—N3—H3B	120.00	H6A—C6—H6B	110.00
C3—N3—H3B	119.00	H6A—C6—H6C	109.00
C3—N3—H3A	119.00	S1—C6—H6C	109.00
C5—N4—H4A	116.00	H6B—C6—H6C	109.00
C8—N4—H4A	116.00	S2—C9—H9B	109.00
S1—C1—N1	119.69 (11)	C8—C9—H9A	109.00
S1—C1—C2	116.86 (10)	S2—C9—H9A	109.00
N1—C1—C2	123.45 (13)	H9A—C9—H9B	108.00
C1—C2—C3	119.22 (12)	C8—C9—H9B	109.00
C1—C2—C7	120.40 (13)	S2—C10—H10A	109.00
C3—C2—C7	120.38 (12)	C11—C10—H10A	109.00
N3—C3—C4	121.32 (13)	C11—C10—H10B	109.00
N3—C3—C2	121.69 (12)	H10A—C10—H10B	108.00
C2—C3—C4	116.98 (12)	S2—C10—H10B	109.00
C3—C4—C5	118.29 (13)	O3—C12—H12A	110.00
N1—C5—N4	110.75 (11)	C13—C12—H12A	110.00
N4—C5—C4	124.09 (13)	C13—C12—H12B	110.00
N1—C5—C4	125.16 (12)	O3—C12—H12B	110.00
N2—C7—C2	178.60 (17)	H12A—C12—H12B	108.00
O1—C8—C9	123.62 (13)	C12—C13—H13B	110.00
O1—C8—N4	123.88 (12)	C12—C13—H13C	109.00
N4—C8—C9	112.49 (12)	C12—C13—H13A	109.00
S2—C9—C8	114.23 (10)	H13A—C13—H13C	109.00
S2—C10—C11	111.95 (10)	H13B—C13—H13C	109.00
O3—C11—C10	110.84 (12)	H13A—C13—H13B	109.00
O2—C11—O3	123.32 (13)
C6—S1—C1—N1	−0.35 (15)	S1—C1—C2—C7	−2.41 (19)
C6—S1—C1—C2	−179.63 (14)	N1—C1—C2—C3	−1.0 (2)
C10—S2—C9—C8	−83.84 (12)	N1—C1—C2—C7	178.34 (14)
C9—S2—C10—C11	63.79 (12)	C1—C2—C3—N3	−179.28 (14)
C12—O3—C11—O2	−4.3 (2)	C1—C2—C3—C4	2.2 (2)
C12—O3—C11—C10	174.39 (12)	C7—C2—C3—N3	1.4 (2)
C11—O3—C12—C13	177.43 (13)	C7—C2—C3—C4	−177.10 (14)
C5—N1—C1—S1	−179.33 (11)	N3—C3—C4—C5	179.07 (14)
C5—N1—C1—C2	−0.1 (2)	C2—C3—C4—C5	−2.4 (2)
C1—N1—C5—N4	179.28 (13)	C3—C4—C5—N1	1.5 (2)
C1—N1—C5—C4	−0.2 (2)	C3—C4—C5—N4	−177.88 (13)
C8—N4—C5—N1	174.69 (14)	O1—C8—C9—S2	−13.0 (2)
C8—N4—C5—C4	−5.9 (2)	N4—C8—C9—S2	168.00 (10)
C5—N4—C8—O1	−3.9 (2)	S2—C10—C11—O2	86.96 (18)
C5—N4—C8—C9	175.09 (13)	S2—C10—C11—O3	−91.73 (13)
S1—C1—C2—C3	178.25 (11)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N2i	0.91	2.43	3.3291 (18)	168
N3—H3B···O1ii	0.91	2.03	2.9345 (18)	177
N4—H4A···O4	0.91	2.01	2.9212 (16)	174
O4—H4B···N2iii	0.84	2.17	3.0032 (19)	172
O4—H4C···O2iv	0.84	2.09	2.9122 (18)	168
C4—H4···O1	0.95	2.25	2.8484 (17)	121

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯N2i	0.91	2.43	3.3291 (18)	168
N3—H3B⋯O1ii	0.91	2.03	2.9345 (18)	177
N4—H4A⋯O4	0.91	2.01	2.9212 (16)	174
O4—H4B⋯N2iii	0.84	2.17	3.0032 (19)	172
O4—H4C⋯O2iv	0.84	2.09	2.9122 (18)	168
C4—H4⋯O1	0.95	2.25	2.8484 (17)	121

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .