research communications
Crystal structures of 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(2,4-dimethylphenyl)acetamide and 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(3-methoxyphenyl)acetamide
aCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India, and bDepartment of Pharmaceutical Science and Technology, Birla Institute of Technology, Mesta, Ranchi 835 215, Jharkhand, India
*Correspondence e-mail: shirai2011@gmail.com
In the title compounds, C14H17N5OS (I) and C13H15N5O2S (II), the dihedral angle between the pyrimidine and benzene rings is 58.64 (8)° in (I) and 78.33 (9)° in (II). In both compounds, there is an intramolecular C—H⋯O hydrogen bond, and in (II) there is also an intramolecular N—H⋯N hydrogen bond present. In the crystals of both compounds, a pair of N—H⋯N hydrogen bonds links the individual molecules to form inversion dimers with R22(8) ring motifs. In (I), the dimers are linked by N—H⋯O and C—H⋯O hydrogen bonds, enclosing R21(14), R21(11) and R21(7) ring motifs, forming layers parallel to the (100) plane. There is also an N—H⋯π interaction present within the layer. In (II), the inversion dimers are linked by N—H⋯O hydrogen bonds enclosing an R44(18) ring motif. The presence of N—H⋯O and C—H⋯O hydrogen bonds generate an R21(6) ring motif. The combination of these various hydrogen bonds results in the formation of layers parallel to the (1-11) plane.
1. Chemical context
Diaminopyrimidine derivatives have been proved to be an important class of compounds because of their therapeutic and pharmacological properties. One such important property is its inhibition potency against cancer targets. As a result of the limited capacity of drugs that can cure or at least prolong the survival of cancer patients, there is always an strong requirement for new chemotherapeutics. It has been reported that diaminopyrimidines show inhibition against cyclin-dependent kinases (cdks), thus arresting cell proliferation in cancer cells (Mesguiche et al., 2003). 2,4-Diaminopyrimidine derivatives have also shown effective suppression of anaplastic lymphoma kinase (ALK), one of the receptor tyrosine kinases that is involved in a variety of tumours (Achary et al., 2017). 2,4-Diaminopyrimidine derivatives have also been reported to exhibit potent inhibitory activity against influenza viruses (Kimura et al., 2006) and have anti-retroviral activity (Hocková et al., 2004), anti-bacterial (Kandeel et al., 1994) and potential anti-microbial properties (Holla et al., 2006). Several diaminopyrimidine derivatives have shown good activity, efficiency against the malarial parasite Plasmodium falciparum K1 strain (Phuangsawai et al., 2016; Chiang et al., 2009). Interestingly, they also act as calcium channel blocking agents (Manjula et al., 2004; Singh et al., 2009). As part of our own studies in this area, we report herein on the syntheses and analyses of the title compounds, 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(2,4-dimethylphenyl)acetamide (I) and [2-((4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(3-methoxyphenyl)acetamide (II).
2. Structural commentary
The molecular structures of compounds (I) and (II) are shown in Figs. 1 and 2, respectively. Compound (I) crystallizes in the monoclinic P21/c and compound (II) in the triclinic P. In compounds (I) and (II), the diaminopyrimidine and benzene rings are inclined to one another by 58.64 (8) and 78.33 (9)°, respectively. The torsion angle C4—S1—C5—C6 = 98.12 (11) ° in compound (I) and −80.14 (14) ° in compound (II), torsion angles S1—C5—C6—N5 = −101.92 (14) ° in compound (I) and 82.23 (16) ° in compound (II), and C5—C6—N5—C7 = 178.66 (15)° in compound (I) and −172.71 (14) ° in compound (II). The bond lengths C4—S1 = 1.7650 (14) Å and C5—S1 = 1.8053 (16) Å in compound (I), and C4—S1 = 1.7721 (17) Å and C5—S1 = 1.8126 (18) Å in compound (II), are comparable with the values reported for a similar structure, 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(2-methylphenyl)acetamide, viz. 1.763 and 1.805 Å, respectively (Subasri et al., 2014). In compound (I), atoms C13 and C14 deviate from the benzene ring by 0.010 (3) and 0.012 (3) Å, respectively. Atoms N1 and N2 deviate from the mean plane of the pyrimidine ring by −0.0819 (18) and 0.0636 (14) Å, respectively, in compound (I), and by 0.0360 (3) and 0.0273 (3) Å, respectively, in compound (II). In both compounds, an intramolecular hydrogen bond, C8—H8⋯O1, forms an S(6) ring motif, and in compound (II) there is also an intramolecular N—H⋯N hydrogen bond present that forms an S(7) ring motif (see Tables 1 and 2).
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3. Supramolecular features
The hydrogen-bonding geometry of compounds (I) and (II) are given in Tables 1 and 2, respectively. In compound (I), atom O1 is a triple acceptor of hydrogen bonds. The N5—H5⋯O1ii hydrogen bonds form a chain running along the c-axis direction. The N2—H2A⋯O1ii and C13—H13C⋯O1ii hydrogen bonds generate an R21(14) ring motif, and the N2—H2A⋯O1ii and N5—H5⋯O1ii hydrogen bonds form an R21(11) ring motif, and N5—H5⋯O1ii and C13—H13⋯O1ii hydrogen bonds generate an R21(7) ring motif (Table 1 and Fig. 3). There is also a N2—H2B⋯π interaction present within the layer (Table 1 and Fig. 4), with the separation distance between the donor and acceptor, Cg1, being 3.4851 (1) Å. The N1—H1A⋯N3i hydrogen bond generates an inversion dimer with an R22(8) ring motif (Table 1 and Fig. 5). As a result of the hydrogen bonding, layers parallel to the bc plane are formed.
In compound (II), atom O2 is a double acceptor of hydrogen bonds. The N2—H2B⋯O2iii hydrogen bond forms an R22(26) ring motif and hydrogen bond C2—H2⋯O2iii generates an R22(26) ring motif (Table 2 and Fig. 6). These two intermolecular hydrogen bonds generate an R21(6) ring motif, which is shown in Fig. 6. Molecules are linked by a pair of N1—H1A⋯N3i hydrogen bonds, forming an inversion dimer with an R22(8) ring motif, and hydrogen bonds N1—H1B⋯O1ii and N1—H1A⋯N3i generate an R44(18) ring motif (Table 2 and Fig. 7). The combination of these various hydrogen bonds results in the formation of layers parallel to (11).
4. Database survey
A search of the Cambridge Structure Database (Version 5.37, update May 2016; Groom et al., 2016) for 2-[(pyrimidine-2-yl)sulfanyl]-N-phenylacetamide yielded seven hits. Three of these involve (4,6-diaminopyrmidin-2-yl) groups. They include the 2-methylphenyl analogue, 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(2-methylphenyl)acetamide (GOKWIO; Subasri et al., 2014), the 2-chlorophenyl analogue, N-(2-chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl) sulfanyl]acetamide (ARARUI; Subasri et al., 2016) and the 3-nitrophenyl analogue, 2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]-N-(3-nitrophenyl)acetamide (ARAROC; Subasri et al., 2016). Here the pyrimidine and benzene rings are inclined to one another by 54.73, 67.11 and 56.19°, respectively, compared to 58.64 (8) ° in compound (I), and 78.33 (9) ° in compound (II).
5. Synthesis and crystallization
Compound (I): To a solution of 4,6-diamino-pyrimidine-2-thiol (0.5 g, 3.52 mmol) in 25 ml of ethanol in a round-bottom flask, potassium hydroxide (0.2 g, 3.52 mmol) was added and the mixture was refluxed for 30 min. 2,4-Dimethylphenyl acetamide (3.52 mmol) was added and the mixture was refluxed for 3 h. At the end of the reaction (observed by TLC), the ethanol was evaporated under vacuum and cold water was added. The precipitate formed was filtered and dried to give compound (I) as a crystalline powder (yield 67%). After purification, the compound was recrystallized from ethanol solution by slow evaporation of the solvent.
Compound (II): To a solution of 4,6-diamino-pyrimidine-2-thiol (0.5 g, 3.52 mmol) in 25 ml of ethanol in a round-bottom flask was added potassium hydroxide (0.2 g, 3.52 mmol) and the mixture was refluxed for 30 min. 3-Methoxyphenyl acetamide (3.52 mmol) was added and the mixture was refluxed for 3 h. At the end of the reaction (observed by TLC), the ethanol was evaporated under vacuum and cold water was added, and the precipitate formed was filtered and dried to give compound (II) as a shiny powder (yield 73%). After purification, the compound was recrystallized from ethanol solution by slow evaporation of the solvent.
6. Refinement
Crystal data, data collection and structure . For both compounds the hydrogen atoms were placed in calculated positions and refined using the riding model: C—H = 0.93–0.97 Å and N—H = 0.86 Å, with Uiso(H) = 1.5Ueq(C-methyl) and 1.2Ueq(N,C) for other H atoms.
details are summarized in Table 3
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Supporting information
https://doi.org/10.1107/S2056989017008143/su5373sup1.cif
contains datablocks global, I, II. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017008143/su5373Isup2.hkl
Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989017008143/su5373IIsup3.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989017008143/su5373Isup4.cml
Supporting information file. DOI: https://doi.org/10.1107/S2056989017008143/su5373IIsup5.cml
For both compounds, data collection: APEX2 (Bruker, 2008); cell
SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: SHELXL2016 (Sheldrick, 2015) and PLATON (Spek, 2009).C14H17N5OS | F(000) = 640 |
Mr = 303.38 | Dx = 1.331 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 23.7716 (6) Å | Cell parameters from 3705 reflections |
b = 7.0073 (2) Å | θ = 1.7–28.3° |
c = 9.0909 (2) Å | µ = 0.22 mm−1 |
β = 90.086 (2)° | T = 293 K |
V = 1514.31 (7) Å3 | Block, yellow |
Z = 4 | 0.24 × 0.18 × 0.12 mm |
Bruker SMART APEXII area-detector diffractometer | 2750 reflections with I > 2σ(I) |
ω and φ scans | Rint = 0.022 |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | θmax = 28.3°, θmin = 1.7° |
Tmin = 0.785, Tmax = 0.854 | h = −31→31 |
13879 measured reflections | k = −8→9 |
3705 independent reflections | l = −12→11 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.040 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.119 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0584P)2 + 0.2187P] where P = (Fo2 + 2Fc2)/3 |
3705 reflections | (Δ/σ)max < 0.001 |
192 parameters | Δρmax = 0.22 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.13091 (2) | 0.71159 (6) | 0.94117 (5) | 0.05991 (16) | |
N4 | 0.15430 (5) | 1.00969 (16) | 0.76929 (12) | 0.0459 (3) | |
N3 | 0.06610 (5) | 0.99914 (17) | 0.89584 (13) | 0.0492 (3) | |
C4 | 0.11650 (6) | 0.9332 (2) | 0.85688 (15) | 0.0434 (3) | |
O1 | 0.25886 (5) | 0.58619 (18) | 1.04523 (13) | 0.0688 (4) | |
C6 | 0.24589 (6) | 0.6857 (2) | 0.94031 (15) | 0.0464 (3) | |
N2 | 0.17546 (7) | 1.2451 (2) | 0.60612 (15) | 0.0646 (4) | |
H2A | 0.206833 | 1.186878 | 0.592034 | 0.078* | |
H2B | 0.168182 | 1.348669 | 0.559012 | 0.078* | |
N5 | 0.27421 (5) | 0.84155 (19) | 0.89770 (15) | 0.0563 (3) | |
H5 | 0.261074 | 0.898941 | 0.821415 | 0.068* | |
C1 | 0.13761 (7) | 1.1740 (2) | 0.70222 (15) | 0.0492 (4) | |
C3 | 0.05202 (7) | 1.1694 (2) | 0.83485 (18) | 0.0547 (4) | |
C2 | 0.08687 (8) | 1.2589 (2) | 0.73351 (18) | 0.0577 (4) | |
H2 | 0.076240 | 1.372376 | 0.688329 | 0.069* | |
C13 | 0.30123 (8) | 1.2195 (2) | 0.8120 (2) | 0.0647 (5) | |
H13A | 0.314436 | 1.348741 | 0.806118 | 0.097* | |
H13B | 0.262823 | 1.218807 | 0.844537 | 0.097* | |
H13C | 0.303624 | 1.160894 | 0.716785 | 0.097* | |
C5 | 0.19468 (6) | 0.6392 (2) | 0.84913 (17) | 0.0503 (4) | |
H5A | 0.193461 | 0.502920 | 0.830692 | 0.060* | |
H5B | 0.197259 | 0.703824 | 0.755023 | 0.060* | |
C12 | 0.33675 (7) | 1.1105 (3) | 0.91894 (17) | 0.0562 (4) | |
C7 | 0.32294 (7) | 0.9247 (3) | 0.96134 (18) | 0.0565 (4) | |
N1 | 0.00214 (7) | 1.2404 (2) | 0.8769 (2) | 0.0826 (5) | |
H1A | −0.018358 | 1.178344 | 0.938385 | 0.099* | |
H1B | −0.009323 | 1.347810 | 0.842366 | 0.099* | |
C11 | 0.38453 (8) | 1.1920 (3) | 0.9800 (2) | 0.0705 (5) | |
H11 | 0.394129 | 1.315535 | 0.952417 | 0.085* | |
C8 | 0.35657 (8) | 0.8271 (3) | 1.0617 (2) | 0.0766 (6) | |
H8 | 0.347527 | 0.703240 | 1.089668 | 0.092* | |
C10 | 0.41862 (8) | 1.0979 (4) | 1.0800 (2) | 0.0808 (6) | |
C9 | 0.40379 (8) | 0.9168 (4) | 1.1195 (3) | 0.0893 (7) | |
H9 | 0.425969 | 0.851470 | 1.187178 | 0.107* | |
C14 | 0.47024 (9) | 1.1953 (5) | 1.1442 (3) | 0.1146 (10) | |
H14A | 0.475144 | 1.156141 | 1.244577 | 0.172* | |
H14B | 0.465342 | 1.331180 | 1.140249 | 0.172* | |
H14C | 0.502847 | 1.160063 | 1.088224 | 0.172* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0529 (3) | 0.0458 (2) | 0.0810 (3) | 0.00850 (17) | 0.00160 (19) | 0.01998 (19) |
N4 | 0.0599 (8) | 0.0368 (6) | 0.0410 (6) | 0.0054 (5) | −0.0075 (5) | −0.0003 (5) |
N3 | 0.0506 (7) | 0.0421 (7) | 0.0548 (7) | 0.0071 (5) | −0.0109 (5) | 0.0004 (5) |
C4 | 0.0536 (8) | 0.0356 (7) | 0.0410 (7) | 0.0034 (6) | −0.0147 (6) | −0.0033 (5) |
O1 | 0.0774 (8) | 0.0705 (8) | 0.0585 (7) | −0.0070 (6) | −0.0125 (6) | 0.0206 (6) |
C6 | 0.0516 (8) | 0.0440 (8) | 0.0435 (7) | 0.0096 (6) | 0.0034 (6) | −0.0017 (6) |
N2 | 0.0844 (11) | 0.0560 (8) | 0.0535 (8) | 0.0111 (7) | −0.0005 (7) | 0.0154 (6) |
N5 | 0.0545 (8) | 0.0549 (8) | 0.0594 (8) | −0.0026 (6) | −0.0117 (6) | 0.0135 (6) |
C1 | 0.0680 (10) | 0.0419 (8) | 0.0376 (7) | 0.0041 (7) | −0.0122 (6) | −0.0001 (6) |
C3 | 0.0606 (10) | 0.0471 (9) | 0.0565 (9) | 0.0121 (7) | −0.0149 (7) | 0.0009 (7) |
C2 | 0.0735 (11) | 0.0445 (8) | 0.0549 (9) | 0.0145 (7) | −0.0132 (8) | 0.0076 (7) |
C13 | 0.0729 (12) | 0.0532 (10) | 0.0679 (11) | −0.0045 (8) | 0.0029 (9) | 0.0017 (8) |
C5 | 0.0584 (9) | 0.0348 (7) | 0.0577 (9) | 0.0078 (6) | −0.0064 (7) | −0.0034 (6) |
C12 | 0.0504 (9) | 0.0651 (11) | 0.0530 (9) | −0.0023 (7) | 0.0089 (7) | −0.0082 (7) |
C7 | 0.0469 (8) | 0.0662 (11) | 0.0564 (9) | 0.0006 (7) | −0.0009 (7) | 0.0014 (8) |
N1 | 0.0686 (10) | 0.0731 (11) | 0.1062 (13) | 0.0325 (8) | 0.0045 (9) | 0.0260 (9) |
C11 | 0.0574 (10) | 0.0841 (14) | 0.0700 (11) | −0.0136 (9) | 0.0119 (9) | −0.0166 (10) |
C8 | 0.0549 (11) | 0.0888 (15) | 0.0860 (13) | 0.0017 (10) | −0.0144 (9) | 0.0159 (11) |
C10 | 0.0484 (10) | 0.1182 (19) | 0.0758 (13) | −0.0087 (11) | 0.0010 (9) | −0.0205 (12) |
C9 | 0.0524 (11) | 0.127 (2) | 0.0887 (15) | 0.0051 (12) | −0.0168 (10) | 0.0071 (14) |
C14 | 0.0601 (13) | 0.167 (3) | 0.117 (2) | −0.0246 (15) | −0.0090 (12) | −0.0338 (19) |
S1—C4 | 1.7650 (14) | C13—H13B | 0.9600 |
S1—C5 | 1.8053 (16) | C13—H13C | 0.9600 |
N4—C4 | 1.3157 (19) | C5—H5A | 0.9700 |
N4—C1 | 1.3616 (18) | C5—H5B | 0.9700 |
N3—C4 | 1.3325 (19) | C12—C11 | 1.386 (2) |
N3—C3 | 1.3577 (19) | C12—C7 | 1.397 (3) |
O1—C6 | 1.2209 (17) | C7—C8 | 1.391 (2) |
C6—N5 | 1.340 (2) | N1—H1A | 0.8600 |
C6—C5 | 1.507 (2) | N1—H1B | 0.8600 |
N2—C1 | 1.350 (2) | C11—C10 | 1.384 (3) |
N2—H2A | 0.8600 | C11—H11 | 0.9300 |
N2—H2B | 0.8600 | C8—C9 | 1.389 (3) |
N5—C7 | 1.419 (2) | C8—H8 | 0.9300 |
N5—H5 | 0.8600 | C10—C9 | 1.365 (3) |
C1—C2 | 1.375 (2) | C10—C14 | 1.520 (3) |
C3—N1 | 1.342 (2) | C9—H9 | 0.9300 |
C3—C2 | 1.389 (2) | C14—H14A | 0.9600 |
C2—H2 | 0.9300 | C14—H14B | 0.9600 |
C13—C12 | 1.496 (2) | C14—H14C | 0.9600 |
C13—H13A | 0.9600 | ||
C4—S1—C5 | 102.04 (7) | S1—C5—H5A | 109.4 |
C4—N4—C1 | 114.62 (13) | C6—C5—H5B | 109.4 |
C4—N3—C3 | 114.68 (14) | S1—C5—H5B | 109.4 |
N4—C4—N3 | 129.41 (13) | H5A—C5—H5B | 108.0 |
N4—C4—S1 | 119.27 (11) | C11—C12—C7 | 117.76 (17) |
N3—C4—S1 | 111.33 (11) | C11—C12—C13 | 120.75 (17) |
O1—C6—N5 | 124.39 (14) | C7—C12—C13 | 121.48 (15) |
O1—C6—C5 | 120.58 (14) | C8—C7—C12 | 120.26 (16) |
N5—C6—C5 | 115.02 (13) | C8—C7—N5 | 122.22 (17) |
C1—N2—H2A | 120.0 | C12—C7—N5 | 117.53 (14) |
C1—N2—H2B | 120.0 | C3—N1—H1A | 120.0 |
H2A—N2—H2B | 120.0 | C3—N1—H1B | 120.0 |
C6—N5—C7 | 128.82 (13) | H1A—N1—H1B | 120.0 |
C6—N5—H5 | 115.6 | C10—C11—C12 | 123.1 (2) |
C7—N5—H5 | 115.6 | C10—C11—H11 | 118.5 |
N2—C1—N4 | 114.07 (14) | C12—C11—H11 | 118.5 |
N2—C1—C2 | 124.03 (14) | C9—C8—C7 | 119.3 (2) |
N4—C1—C2 | 121.90 (15) | C9—C8—H8 | 120.4 |
N1—C3—N3 | 115.25 (16) | C7—C8—H8 | 120.4 |
N1—C3—C2 | 123.37 (15) | C9—C10—C11 | 117.66 (18) |
N3—C3—C2 | 121.35 (15) | C9—C10—C14 | 121.7 (2) |
C1—C2—C3 | 117.79 (14) | C11—C10—C14 | 120.7 (2) |
C1—C2—H2 | 121.1 | C10—C9—C8 | 122.0 (2) |
C3—C2—H2 | 121.1 | C10—C9—H9 | 119.0 |
C12—C13—H13A | 109.5 | C8—C9—H9 | 119.0 |
C12—C13—H13B | 109.5 | C10—C14—H14A | 109.5 |
H13A—C13—H13B | 109.5 | C10—C14—H14B | 109.5 |
C12—C13—H13C | 109.5 | H14A—C14—H14B | 109.5 |
H13A—C13—H13C | 109.5 | C10—C14—H14C | 109.5 |
H13B—C13—H13C | 109.5 | H14A—C14—H14C | 109.5 |
C6—C5—S1 | 111.24 (10) | H14B—C14—H14C | 109.5 |
C6—C5—H5A | 109.4 | ||
C1—N4—C4—N3 | −4.6 (2) | N5—C6—C5—S1 | −101.92 (14) |
C1—N4—C4—S1 | 175.79 (10) | C4—S1—C5—C6 | 98.12 (11) |
C3—N3—C4—N4 | 0.5 (2) | C11—C12—C7—C8 | 0.0 (3) |
C3—N3—C4—S1 | −179.87 (10) | C13—C12—C7—C8 | −179.62 (17) |
C5—S1—C4—N4 | −8.96 (12) | C11—C12—C7—N5 | −179.55 (15) |
C5—S1—C4—N3 | 171.36 (10) | C13—C12—C7—N5 | 0.8 (2) |
O1—C6—N5—C7 | −0.7 (3) | C6—N5—C7—C8 | 15.4 (3) |
C5—C6—N5—C7 | 178.66 (15) | C6—N5—C7—C12 | −165.04 (15) |
C4—N4—C1—N2 | −176.34 (12) | C7—C12—C11—C10 | −0.1 (3) |
C4—N4—C1—C2 | 4.7 (2) | C13—C12—C11—C10 | 179.58 (17) |
C4—N3—C3—N1 | −177.94 (14) | C12—C7—C8—C9 | 0.3 (3) |
C4—N3—C3—C2 | 3.6 (2) | N5—C7—C8—C9 | 179.83 (18) |
N2—C1—C2—C3 | 179.97 (15) | C12—C11—C10—C9 | −0.2 (3) |
N4—C1—C2—C3 | −1.2 (2) | C12—C11—C10—C14 | −179.48 (19) |
N1—C3—C2—C1 | 178.45 (16) | C11—C10—C9—C8 | 0.5 (3) |
N3—C3—C2—C1 | −3.2 (2) | C14—C10—C9—C8 | 179.8 (2) |
O1—C6—C5—S1 | 77.43 (16) | C7—C8—C9—C10 | −0.6 (4) |
Cg1 is the centroid of the N3/N4/C1–C4 ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
C8—H8···O1 | 0.93 | 2.30 | 2.8752 (1) | 120 |
N1—H1A···N3i | 0.86 | 2.26 | 3.1187 (1) | 175 |
N2—H2A···O1ii | 0.86 | 2.32 | 3.1032 (1) | 152 |
N5—H5···O1ii | 0.86 | 2.51 | 3.2640 (1) | 146 |
C13—H13C···O1ii | 0.96 | 2.56 | 3.3880 (1) | 144 |
N2—H2B···Cg1iii | 0.86 | 2.88 | 3.4851 (1) | 130 |
Symmetry codes: (i) −x, −y+2, −z+2; (ii) x, −y+3/2, z−1/2; (iii) x, −y+3/2, z−3/2. |
C13H15N5O2S | Z = 2 |
Mr = 305.36 | F(000) = 320 |
Triclinic, P1 | Dx = 1.388 Mg m−3 |
a = 8.014 (5) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 8.724 (5) Å | Cell parameters from 2991 reflections |
c = 12.068 (5) Å | θ = 1.8–26.5° |
α = 106.561 (5)° | µ = 0.23 mm−1 |
β = 97.888 (5)° | T = 293 K |
γ = 110.461 (5)° | Block, yellow |
V = 730.9 (7) Å3 | 0.30 × 0.25 × 0.20 mm |
Bruker SMART APEXII area-detector diffractometer | 2616 reflections with I > 2σ(I) |
ω and φ scans | Rint = 0.026 |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | θmax = 26.5°, θmin = 1.8° |
Tmin = 0.785, Tmax = 0.843 | h = −10→9 |
10789 measured reflections | k = −10→10 |
2991 independent reflections | l = −15→15 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.110 | H-atom parameters constrained |
S = 0.81 | w = 1/[σ2(Fo2) + (0.082P)2 + 0.3261P] where P = (Fo2 + 2Fc2)/3 |
2991 reflections | (Δ/σ)max = 0.001 |
191 parameters | Δρmax = 0.17 e Å−3 |
0 restraints | Δρmin = −0.27 e Å−3 |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.2721 (2) | 0.7765 (2) | 0.75950 (14) | 0.0415 (4) | |
C2 | 0.4285 (2) | 0.8303 (2) | 0.72068 (14) | 0.0416 (4) | |
H2 | 0.517868 | 0.944735 | 0.755617 | 0.050* | |
C3 | 0.4481 (2) | 0.70658 (19) | 0.62691 (13) | 0.0371 (3) | |
C4 | 0.1714 (2) | 0.50538 (19) | 0.61966 (13) | 0.0345 (3) | |
C5 | −0.1544 (2) | 0.2625 (2) | 0.63675 (15) | 0.0478 (4) | |
H5A | −0.175956 | 0.368379 | 0.661775 | 0.057* | |
H5B | −0.271283 | 0.165803 | 0.589640 | 0.057* | |
C6 | −0.0831 (2) | 0.2295 (2) | 0.74625 (15) | 0.0451 (4) | |
C7 | 0.1429 (2) | 0.3944 (2) | 0.94683 (13) | 0.0388 (3) | |
C8 | 0.1195 (3) | 0.2573 (2) | 0.98958 (17) | 0.0524 (4) | |
H8 | 0.029765 | 0.145119 | 0.945410 | 0.063* | |
C9 | 0.2324 (3) | 0.2922 (3) | 1.09848 (19) | 0.0610 (5) | |
H9 | 0.217277 | 0.201394 | 1.127299 | 0.073* | |
C10 | 0.3670 (3) | 0.4566 (2) | 1.16652 (17) | 0.0519 (4) | |
H10 | 0.441229 | 0.476596 | 1.239984 | 0.062* | |
C11 | 0.3892 (2) | 0.5915 (2) | 1.12302 (14) | 0.0414 (4) | |
C12 | 0.2776 (2) | 0.5599 (2) | 1.01376 (14) | 0.0397 (3) | |
H12 | 0.293260 | 0.650900 | 0.985061 | 0.048* | |
C13 | 0.6424 (3) | 0.7978 (3) | 1.29014 (18) | 0.0632 (5) | |
H13A | 0.576735 | 0.780929 | 1.349543 | 0.095* | |
H13B | 0.731248 | 0.917131 | 1.317583 | 0.095* | |
H13C | 0.704699 | 0.720780 | 1.276837 | 0.095* | |
N4 | 0.13965 (18) | 0.61019 (17) | 0.70978 (11) | 0.0396 (3) | |
N3 | 0.31604 (17) | 0.54040 (16) | 0.57426 (11) | 0.0368 (3) | |
N2 | 0.2417 (3) | 0.8847 (2) | 0.85299 (15) | 0.0634 (5) | |
H2A | 0.143870 | 0.846000 | 0.876513 | 0.076* | |
H2B | 0.320263 | 0.991812 | 0.888534 | 0.076* | |
N1 | 0.5973 (2) | 0.74522 (19) | 0.58440 (14) | 0.0527 (4) | |
H1A | 0.606000 | 0.666365 | 0.526465 | 0.063* | |
H1B | 0.684496 | 0.848902 | 0.615032 | 0.063* | |
N5 | 0.03559 (19) | 0.37602 (17) | 0.83726 (12) | 0.0425 (3) | |
H5 | 0.047786 | 0.472628 | 0.827087 | 0.051* | |
O1 | −0.1275 (2) | 0.08145 (17) | 0.74876 (13) | 0.0675 (4) | |
O2 | 0.51589 (19) | 0.76002 (16) | 1.18149 (11) | 0.0584 (4) | |
S1 | 0.00691 (5) | 0.28602 (5) | 0.54469 (3) | 0.04131 (14) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0530 (9) | 0.0339 (8) | 0.0391 (8) | 0.0203 (7) | 0.0146 (7) | 0.0113 (6) |
C2 | 0.0476 (9) | 0.0276 (7) | 0.0427 (8) | 0.0118 (6) | 0.0105 (7) | 0.0081 (6) |
C3 | 0.0413 (8) | 0.0308 (7) | 0.0357 (7) | 0.0122 (6) | 0.0090 (6) | 0.0106 (6) |
C4 | 0.0364 (7) | 0.0323 (7) | 0.0323 (7) | 0.0130 (6) | 0.0046 (6) | 0.0113 (6) |
C5 | 0.0302 (7) | 0.0491 (10) | 0.0466 (9) | 0.0049 (7) | 0.0058 (6) | 0.0087 (7) |
C6 | 0.0359 (8) | 0.0407 (9) | 0.0453 (9) | 0.0031 (7) | 0.0145 (7) | 0.0103 (7) |
C7 | 0.0421 (8) | 0.0363 (8) | 0.0376 (8) | 0.0151 (6) | 0.0163 (6) | 0.0115 (6) |
C8 | 0.0598 (10) | 0.0365 (9) | 0.0551 (10) | 0.0112 (8) | 0.0152 (8) | 0.0187 (8) |
C9 | 0.0724 (13) | 0.0485 (10) | 0.0673 (12) | 0.0203 (9) | 0.0154 (10) | 0.0348 (9) |
C10 | 0.0593 (10) | 0.0522 (10) | 0.0500 (10) | 0.0255 (9) | 0.0104 (8) | 0.0248 (8) |
C11 | 0.0459 (8) | 0.0374 (8) | 0.0417 (8) | 0.0201 (7) | 0.0111 (7) | 0.0119 (7) |
C12 | 0.0472 (8) | 0.0330 (8) | 0.0397 (8) | 0.0163 (7) | 0.0127 (7) | 0.0139 (6) |
C13 | 0.0604 (11) | 0.0612 (12) | 0.0535 (11) | 0.0200 (10) | −0.0085 (9) | 0.0171 (9) |
N4 | 0.0433 (7) | 0.0355 (7) | 0.0396 (7) | 0.0161 (6) | 0.0133 (5) | 0.0117 (5) |
N3 | 0.0382 (6) | 0.0315 (6) | 0.0349 (6) | 0.0108 (5) | 0.0090 (5) | 0.0082 (5) |
N2 | 0.0777 (11) | 0.0396 (8) | 0.0652 (10) | 0.0191 (8) | 0.0375 (9) | 0.0052 (7) |
N1 | 0.0504 (8) | 0.0339 (7) | 0.0568 (9) | 0.0046 (6) | 0.0241 (7) | 0.0037 (6) |
N5 | 0.0473 (7) | 0.0336 (7) | 0.0391 (7) | 0.0098 (6) | 0.0117 (6) | 0.0108 (5) |
O1 | 0.0721 (9) | 0.0383 (7) | 0.0593 (8) | −0.0068 (6) | 0.0068 (7) | 0.0129 (6) |
O2 | 0.0670 (8) | 0.0390 (7) | 0.0513 (7) | 0.0153 (6) | −0.0123 (6) | 0.0118 (5) |
S1 | 0.0384 (2) | 0.0372 (2) | 0.0341 (2) | 0.00654 (16) | 0.00462 (15) | 0.00617 (16) |
C1—N4 | 1.358 (2) | C8—C9 | 1.375 (3) |
C1—C2 | 1.374 (2) | C8—H8 | 0.9300 |
C1—N2 | 1.361 (2) | C9—C10 | 1.378 (3) |
C2—C3 | 1.393 (2) | C9—H9 | 0.9300 |
C2—H2 | 0.9300 | C10—C11 | 1.387 (3) |
C3—N1 | 1.339 (2) | C10—H10 | 0.9300 |
C3—N3 | 1.357 (2) | C11—O2 | 1.363 (2) |
C4—N4 | 1.325 (2) | C11—C12 | 1.383 (2) |
C4—N3 | 1.327 (2) | C12—H12 | 0.9300 |
C4—S1 | 1.7721 (17) | C13—O2 | 1.418 (2) |
C5—C6 | 1.510 (3) | C13—H13A | 0.9600 |
C5—S1 | 1.8126 (18) | C13—H13B | 0.9600 |
C5—H5A | 0.9700 | C13—H13C | 0.9600 |
C5—H5B | 0.9700 | N2—H2A | 0.8600 |
C6—O1 | 1.224 (2) | N2—H2B | 0.8600 |
C6—N5 | 1.345 (2) | N1—H1A | 0.8600 |
C7—C12 | 1.381 (2) | N1—H1B | 0.8600 |
C7—C8 | 1.397 (2) | N5—H5 | 0.8600 |
C7—N5 | 1.409 (2) | ||
N4—C1—C2 | 122.38 (14) | C8—C9—H9 | 118.7 |
N4—C1—N2 | 115.28 (15) | C9—C10—C11 | 118.53 (17) |
C2—C1—N2 | 122.31 (16) | C9—C10—H10 | 120.7 |
C1—C2—C3 | 117.36 (14) | C11—C10—H10 | 120.7 |
C1—C2—H2 | 121.3 | O2—C11—C12 | 115.38 (14) |
C3—C2—H2 | 121.3 | O2—C11—C10 | 124.50 (15) |
N1—C3—N3 | 116.77 (14) | C12—C11—C10 | 120.12 (16) |
N1—C3—C2 | 121.86 (14) | C7—C12—C11 | 120.61 (15) |
N3—C3—C2 | 121.37 (14) | C7—C12—H12 | 119.7 |
N4—C4—N3 | 128.70 (14) | C11—C12—H12 | 119.7 |
N4—C4—S1 | 119.42 (12) | O2—C13—H13A | 109.5 |
N3—C4—S1 | 111.88 (11) | O2—C13—H13B | 109.5 |
C6—C5—S1 | 111.79 (12) | H13A—C13—H13B | 109.5 |
C6—C5—H5A | 109.3 | O2—C13—H13C | 109.5 |
S1—C5—H5A | 109.3 | H13A—C13—H13C | 109.5 |
C6—C5—H5B | 109.3 | H13B—C13—H13C | 109.5 |
S1—C5—H5B | 109.3 | C4—N4—C1 | 114.83 (14) |
H5A—C5—H5B | 107.9 | C4—N3—C3 | 115.33 (13) |
O1—C6—N5 | 124.17 (17) | C1—N2—H2A | 120.0 |
O1—C6—C5 | 122.10 (15) | C1—N2—H2B | 120.0 |
N5—C6—C5 | 113.70 (15) | H2A—N2—H2B | 120.0 |
C12—C7—C8 | 119.78 (15) | C3—N1—H1A | 120.0 |
C12—C7—N5 | 116.25 (14) | C3—N1—H1B | 120.0 |
C8—C7—N5 | 123.97 (15) | H1A—N1—H1B | 120.0 |
C9—C8—C7 | 118.46 (17) | C6—N5—C7 | 129.44 (15) |
C9—C8—H8 | 120.8 | C6—N5—H5 | 115.3 |
C7—C8—H8 | 120.8 | C7—N5—H5 | 115.3 |
C10—C9—C8 | 122.51 (17) | C11—O2—C13 | 117.88 (14) |
C10—C9—H9 | 118.7 | C4—S1—C5 | 103.05 (8) |
N4—C1—C2—C3 | −0.1 (2) | S1—C4—N4—C1 | −178.68 (11) |
N2—C1—C2—C3 | 177.81 (16) | C2—C1—N4—C4 | −1.3 (2) |
C1—C2—C3—N1 | −178.60 (15) | N2—C1—N4—C4 | −179.36 (14) |
C1—C2—C3—N3 | 1.3 (2) | N4—C4—N3—C3 | −0.6 (2) |
S1—C5—C6—O1 | −95.98 (18) | S1—C4—N3—C3 | 179.78 (10) |
S1—C5—C6—N5 | 82.23 (16) | N1—C3—N3—C4 | 178.93 (14) |
C12—C7—C8—C9 | 0.2 (3) | C2—C3—N3—C4 | −1.0 (2) |
N5—C7—C8—C9 | −179.56 (17) | O1—C6—N5—C7 | 5.5 (3) |
C7—C8—C9—C10 | 0.0 (3) | C5—C6—N5—C7 | −172.71 (14) |
C8—C9—C10—C11 | −0.1 (3) | C12—C7—N5—C6 | 168.50 (15) |
C9—C10—C11—O2 | 179.53 (18) | C8—C7—N5—C6 | −11.7 (3) |
C9—C10—C11—C12 | 0.1 (3) | C12—C11—O2—C13 | −175.89 (16) |
C8—C7—C12—C11 | −0.2 (2) | C10—C11—O2—C13 | 4.7 (3) |
N5—C7—C12—C11 | 179.57 (14) | N4—C4—S1—C5 | −8.27 (14) |
O2—C11—C12—C7 | −179.39 (14) | N3—C4—S1—C5 | 171.36 (11) |
C10—C11—C12—C7 | 0.1 (2) | C6—C5—S1—C4 | −80.14 (14) |
N3—C4—N4—C1 | 1.8 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N5—H5···N4 | 0.86 | 2.15 | 2.861 (3) | 140 |
C8—H8···O1 | 0.93 | 2.34 | 2.911 (3) | 120 |
N1—H1A···N3i | 0.86 | 2.21 | 3.035 (3) | 162 |
N1—H1B···O1ii | 0.86 | 2.08 | 2.891 (3) | 157 |
N2—H2B···O2iii | 0.86 | 2.55 | 3.210 (3) | 135 |
C2—H2···O2iii | 0.93 | 2.59 | 3.272 (3) | 130 |
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x+1, y+1, z; (iii) −x+1, −y+2, −z+2. |
Acknowledgements
MC thanks CSIR, Government of India, for the SRF fellowship and MC, VV and DV thank TBI X-ray facility, CAS in Crystallography and Biophysics, University of Madras, India, for data collection.
References
Achary, R., Mathi, G. R., Lee, D. H., Yun, C. S., Lee, C. O., Kim, H. R., Park, C. H., Kim, P. & Hwang, J. Y. (2017). Bioorg. Med. Chem. Lett. 27, 2185–2191. Web of Science CrossRef CAS PubMed Google Scholar
Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Chiang, A. N., Valderramos, J. C., Balachandran, R., Chovatiya, R. J., Mead, B. P., Schneider, C., Bell, S. L., Klein, M. G., Huryn, D. M., Chen, X. S., Day, B. W., Fidock, D. A., Wipf, P. & Brodsky, J. L. (2009). Bioorg. Med. Chem. 17, 1527–1533. Web of Science CrossRef PubMed CAS Google Scholar
Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Web of Science CrossRef CAS IUCr Journals Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CSD CrossRef IUCr Journals Google Scholar
Hocková, D., Holý, A. N., Masojídková, M., Andrei, G., Snoeck, R., De Clercq, E. & Balzarini, J. (2004). Bioorg. Med. Chem. 12, 3197–3202. Web of Science PubMed Google Scholar
Holla, B. S., Mahalinga, M., Karthikeyan, M. S., Akberali, P. M. & Shetty, N. S. (2006). Bioorg. Med. Chem. 14, 2040–2047. Web of Science CrossRef PubMed CAS Google Scholar
Kandeel, M., El-Meligie, S., Omar, R., Roshdy, S. & Youssef, K. (1994). J. Pharm. Sci. 3, 197–205. CAS Google Scholar
Kimura, H., Katoh, T., Kajimoto, T., Node, M., Hisaki, M., Sugimoto, Y., Majima, T., Uehara, Y. & Yamori, T. (2006). Anticancer Res. 26, 91–97. Web of Science PubMed CAS Google Scholar
Manjula, A., Rao, V. & Neelakantan, P. (2004). Synth. Commun. 34, 2665–2671. Web of Science CrossRef CAS Google Scholar
Mesguiche, V., Parsons, R. J., Arris, C. E., Bentley, J., Boyle, F. T., Curtin, N. J., Davies, T. G., Endicott, J. A., Gibson, A. E., Golding, B. T., Griffin, R. J., Jewsbury, P., Johnson, L. N., Newell, D. R., Noble, M. E. M., Wang, L. Z. & Hardcastle, I. R. (2003). Bioorg. Med. Chem. Lett. 13, 217–222. Web of Science CrossRef PubMed CAS Google Scholar
Phuangsawai, O., Beswick, P., Ratanabunyong, S., Tabtimmai, L., Suphakun, P., Obounchoey, P., Srisook, P., Horata, N., Chuckowree, I., Hannongbua, S., Ward, S. E., Choowongkomon, K. & Gleeson, M. P. (2016). Eur. J. Med. Chem. 124, 896–905. Web of Science CrossRef CAS PubMed Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Singh, K., Arora, D., Poremsky, E., Lowery, J. & Moreland, R. S. (2009). Eur. J. Med. Chem. 44, 1997–2001. Web of Science CrossRef PubMed CAS Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
Subasri, S., Kumar, T. A., Sinha, B. N., Jayaprakash, V. & Velmurugan, D. (2014). Acta Cryst. E70, o850. CSD CrossRef IUCr Journals Google Scholar
Subasri, S., Timiri, A. K., Barji, N. S., Jayaprakash, V., Vijayan, V. & Velmurugan, D. (2016). Acta Cryst. E72, 1171–1175. Web of Science CSD CrossRef IUCr Journals Google Scholar
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