| Literature DB >> 31921445 |
Alexandre V Ivachtchenko1, Sergiy M Kovalenko1,2, Dmitry V Kravchenko3, Oleg D Mitkin1, Vladimir V Ivanov2, Thierry Langer4.
Abstract
The title compound, C15H22N4O5S, was prepared via alkyl-ation of 3-(chloro-meth-yl)-5-(pentan-3-yl)-1,2,4-oxa-diazole in anhydrous dioxane in the presence of tri-ethyl-amine. The thia-diazine ring has an envelope conformation with the S atom displaced by 0.4883 (6) Å from the mean plane through the other five atoms. The planar 1,2,4-oxa-diazole ring is inclined to the mean plane of the thia-diazine ring by 77.45 (11)°. In the crystal, mol-ecules are linked by C-H⋯N hydrogen bonds, forming chains propagating along the b-axis direction. Hirshfeld surface analysis and two-dimensional fingerprint plots have been used to analyse the inter-molecular contacts present in the crystal. Mol-ecular docking studies were use to evaluate the title compound as a potential system that inter-acts effectively with the capsid of the Hepatitis B virus (HBV), supported by an experimental in vitro HBV replication model. © Ivachtchenko et al. 2020.Entities:
Keywords: 2H-1,2,6-thiadiazine 1,1-dioxide; HBV; Hirshfeld surface analysis; crystal structure; hepatitis B; hydrogen bonding; molecular docking study
Year: 2020 PMID: 31921445 PMCID: PMC6944089 DOI: 10.1107/S2056989019015986
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1Synthesis of 2H-1,2,6-thiadiazine 1,1-dioxide via intermolecular cyclization of sulfamide with the corresponding 1,3-diketone.
Figure 2Synthesis of the title compound 3.
Figure 3The molecular structure of compound 3, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| C4—H4⋯N2i | 0.93 | 2.54 | 3.431 (3) | 161 |
Symmetry code: (i) .
Figure 4A partial view along the a axis of the crystal packing of compound 3. Hydrogen bonds (Table 1 ▸) are shown as dashed lines.
Figure 5The Hirshfeld surface of compound 3, mapped over d norm, with a fixed colour scale of −0.484 to 1.652 a.u.
Short contacts (Å) in the crystal of compound 3
| Atom1⋯Atom2 | Length | Length – vdW |
|---|---|---|
| S1.·H7 | 3.090 | 0.090 |
| O2⋯H7 | 2.813 | 0.093 |
| H7 | 2.687 | −0.033 |
| H12 | 2.772 | 0.022 |
| O4⋯H14 | 2.700 | −0.020 |
| C8⋯H14 | 2.913 | 0.013 |
| C6⋯H10 | 2.978 | 0.078 |
| O2⋯C3v | 3.275 | 0.055 |
| O2⋯H3 | 2.634 | −0.086 |
| O3⋯C4v | 3.077 | −0.143 |
| N2⋯H3 | 2.816 | 0.066 |
| N2⋯H | 2.538 | −0.212 |
| H3 | 2.799 | 0.079 |
Symmetry codes: (i) −x + 1, y − , −z + ; (ii) x − , −y + , −z + 1; (iii) −x + 1, −y + 1, −z + 1; (iv) −x + , y − , z; (v) −x + , y − , z.
Figure 6(a) The two-dimensional fingerprint plot for compound 3, and delineated into (b) H⋯H (48.7%), (c) O⋯H/H⋯O (27.5%), (d) N⋯H/H⋯N (14.9%) and (e) C⋯H/H⋯C (5.2%) contacts.
Binding affinity parameters of title molecule with HBV core proteins
| PDB refcode | Est. binding energy (kcal mol−1) | Binding affinity score |
|---|---|---|
| 5E0I | −14.54 | −25.2 |
| 5GMZ | −14.30 | −14.99 |
| 5WRE | −16.03 | −8.28 |
| 5T2P | −17.05 | −22.34 |
Figure 7Calculated docking poses for the complex ‘title molecule–protein’.
Torsion angles (°) comparison for X-ray, ab and docking data
| Torsion angle | X-ray | M062x/cc-pVDZ | 5E0I | 5GMZ | 5WRE | 5T2P |
|---|---|---|---|---|---|---|
| O2—S1—N4—C6 | 83.5 (2) | 78.7 | 93.13 | 93.2 | 93.1 | 137.4 |
| C5—C8—O5—C9 | 178.4 (2) | 178.9 | −112.9 | −79.3 | −110.4 | −163.1 |
| S1—N3—C3—C2 | −71.7 (2) | −71.5 | −148.5 | −126.7 | −172.5 | −80 |
| O1—C1—C11—C14 | 57.8 (3) | 49.9 | 50.1 | −112.9 | 9.8 | 52.8 |
Figure 8Calculated structure of the title compound.
Experimental details
| Crystal data | |
| Chemical formula | C15H22N4O5S |
|
| 370.42 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 293 |
|
| 12.4962 (5), 9.9237 (4), 29.5925 (15) |
|
| 3669.7 (3) |
|
| 8 |
| Radiation type | Mo |
| μ (mm−1) | 0.21 |
| Crystal size (mm) | 0.4 × 0.2 × 0.1 |
| Data collection | |
| Diffractometer | Rigaku Oxford Diffraction Xcalibur, Sapphire3 |
| Absorption correction | Multi-scan ( |
|
| 0.466, 1.000 |
| No. of measured, independent and observed [ | 26547, 3211, 2510 |
|
| 0.070 |
| (sin θ/λ)max (Å−1) | 0.595 |
| Refinement | |
|
| 0.050, 0.127, 1.06 |
| No. of reflections | 3211 |
| No. of parameters | 230 |
| H-atom treatment | H-atom parameters constrained |
| Δρmax, Δρmin (e Å−3) | 0.24, −0.32 |
Computer programs: CrysAlis PRO (Rigaku OD, 2018 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL (Sheldrick, 2015b ▸), OLEX2 (Dolomanov et al., 2009 ▸), Mercury (Macrae et al., 2008 ▸), PLATON (Spek, 2009 ▸) and publCIF (Westrip, 2010 ▸).
| C15H22N4O5S | |
| Mo | |
| Orthorhombic, | Cell parameters from 3271 reflections |
| θ = 3.6–23.3° | |
| µ = 0.21 mm−1 | |
| Block, colourless | |
| 0.4 × 0.2 × 0.1 mm | |
| Rigaku Oxford Diffraction Xcalibur, Sapphire3 diffractometer | 3211 independent reflections |
| Radiation source: fine-focus sealed X-ray tube, Enhance (Mo) X-ray Source | 2510 reflections with |
| Graphite monochromator | |
| Detector resolution: 16.1827 pixels mm-1 | θmax = 25.0°, θmin = 3.0° |
| ω scans | |
| Absorption correction: multi-scan (CrysAlis PRO; Rigaku OD, 2018) | |
| 26547 measured reflections |
| Refinement on | Primary atom site location: dual |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| Hydrogen site location: difference Fourier map | |
| H-atom parameters constrained | |
| 3211 reflections | (Δ/σ)max < 0.001 |
| 230 parameters | Δρmax = 0.24 e Å−3 |
| 0 restraints | Δρmin = −0.32 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. |
| S1 | 0.66349 (5) | 0.40561 (6) | 0.31677 (2) | 0.0462 (2) | |
| O1 | 0.74895 (14) | 0.29562 (18) | 0.46836 (6) | 0.0577 (5) | |
| O2 | 0.60666 (16) | 0.31342 (17) | 0.34444 (7) | 0.0646 (6) | |
| O3 | 0.76374 (15) | 0.3626 (2) | 0.30037 (8) | 0.0726 (6) | |
| O4 | 0.47430 (16) | 0.86020 (18) | 0.34934 (7) | 0.0668 (6) | |
| O5 | 0.35185 (14) | 0.7296 (2) | 0.31536 (7) | 0.0654 (6) | |
| N1 | 0.65072 (15) | 0.4628 (2) | 0.44365 (7) | 0.0472 (5) | |
| N2 | 0.80748 (16) | 0.3561 (2) | 0.43291 (8) | 0.0514 (5) | |
| N3 | 0.68614 (14) | 0.54419 (19) | 0.34784 (7) | 0.0415 (5) | |
| N4 | 0.58953 (16) | 0.4585 (2) | 0.27686 (7) | 0.0495 (5) | |
| C1 | 0.65689 (19) | 0.3647 (2) | 0.47179 (9) | 0.0463 (6) | |
| C2 | 0.74512 (17) | 0.4525 (2) | 0.42013 (8) | 0.0402 (5) | |
| C3 | 0.77420 (18) | 0.5405 (2) | 0.38103 (9) | 0.0467 (6) | |
| H3A | 0.788916 | 0.631017 | 0.391704 | 0.056* | |
| H3B | 0.838461 | 0.506142 | 0.366693 | 0.056* | |
| C4 | 0.61014 (18) | 0.6400 (2) | 0.34937 (8) | 0.0427 (6) | |
| H4 | 0.615584 | 0.705875 | 0.371592 | 0.051* | |
| C5 | 0.52574 (18) | 0.6464 (2) | 0.32039 (8) | 0.0412 (6) | |
| C6 | 0.52217 (19) | 0.5588 (2) | 0.28224 (9) | 0.0457 (6) | |
| C7 | 0.4479 (2) | 0.5814 (3) | 0.24327 (10) | 0.0660 (8) | |
| H7A | 0.471161 | 0.528646 | 0.217909 | 0.099* | |
| H7B | 0.448204 | 0.675101 | 0.235238 | 0.099* | |
| H7C | 0.376781 | 0.554846 | 0.251685 | 0.099* | |
| C8 | 0.4500 (2) | 0.7587 (3) | 0.32946 (9) | 0.0497 (6) | |
| C9 | 0.2702 (2) | 0.8316 (4) | 0.32370 (14) | 0.0881 (11) | |
| H9A | 0.275933 | 0.864784 | 0.354432 | 0.106* | |
| H9B | 0.279751 | 0.906902 | 0.303192 | 0.106* | |
| C10 | 0.1671 (3) | 0.7707 (5) | 0.31670 (19) | 0.1275 (19) | |
| H10A | 0.163950 | 0.732718 | 0.286891 | 0.191* | |
| H10B | 0.112282 | 0.837879 | 0.319856 | 0.191* | |
| H10C | 0.156092 | 0.700900 | 0.338674 | 0.191* | |
| C11 | 0.5779 (2) | 0.3135 (3) | 0.50547 (10) | 0.0601 (7) | |
| H11 | 0.517153 | 0.375927 | 0.506023 | 0.072* | |
| C12 | 0.5362 (3) | 0.1749 (3) | 0.49009 (12) | 0.0756 (9) | |
| H12A | 0.596527 | 0.113804 | 0.487578 | 0.091* | |
| H12B | 0.489029 | 0.139689 | 0.513284 | 0.091* | |
| C13 | 0.4770 (3) | 0.1756 (4) | 0.44585 (14) | 0.0939 (12) | |
| H13A | 0.522406 | 0.211801 | 0.422662 | 0.141* | |
| H13B | 0.413982 | 0.230344 | 0.448575 | 0.141* | |
| H13C | 0.456836 | 0.085211 | 0.438077 | 0.141* | |
| C14 | 0.6254 (3) | 0.3084 (3) | 0.55267 (11) | 0.0799 (10) | |
| H14A | 0.572775 | 0.269913 | 0.573035 | 0.096* | |
| H14B | 0.686816 | 0.248710 | 0.552328 | 0.096* | |
| C15 | 0.6597 (3) | 0.4429 (4) | 0.57096 (13) | 0.1016 (13) | |
| H15A | 0.714439 | 0.480074 | 0.551891 | 0.152* | |
| H15B | 0.687317 | 0.431690 | 0.601003 | 0.152* | |
| H15C | 0.599454 | 0.502798 | 0.571657 | 0.152* |
| S1 | 0.0472 (4) | 0.0396 (4) | 0.0518 (4) | 0.0034 (3) | −0.0079 (3) | 0.0008 (3) |
| O1 | 0.0566 (11) | 0.0612 (11) | 0.0553 (12) | 0.0133 (9) | 0.0089 (9) | 0.0161 (9) |
| O2 | 0.0825 (14) | 0.0438 (10) | 0.0674 (13) | −0.0180 (10) | −0.0177 (11) | 0.0143 (9) |
| O3 | 0.0531 (11) | 0.0764 (13) | 0.0881 (16) | 0.0224 (10) | −0.0045 (11) | −0.0190 (12) |
| O4 | 0.0760 (13) | 0.0518 (11) | 0.0725 (15) | 0.0144 (10) | 0.0007 (11) | −0.0081 (10) |
| O5 | 0.0439 (10) | 0.0727 (13) | 0.0796 (15) | 0.0152 (9) | 0.0022 (9) | −0.0008 (10) |
| N1 | 0.0432 (11) | 0.0428 (11) | 0.0555 (14) | 0.0035 (9) | 0.0051 (10) | 0.0075 (10) |
| N2 | 0.0458 (11) | 0.0587 (13) | 0.0497 (14) | 0.0063 (10) | 0.0053 (10) | 0.0090 (10) |
| N3 | 0.0394 (10) | 0.0387 (11) | 0.0463 (12) | −0.0029 (9) | −0.0046 (9) | 0.0043 (9) |
| N4 | 0.0549 (12) | 0.0466 (12) | 0.0470 (13) | 0.0060 (10) | −0.0082 (10) | −0.0014 (9) |
| C1 | 0.0476 (14) | 0.0438 (14) | 0.0474 (16) | 0.0064 (11) | 0.0042 (11) | 0.0003 (11) |
| C2 | 0.0353 (12) | 0.0417 (12) | 0.0435 (14) | −0.0036 (10) | −0.0049 (10) | −0.0006 (10) |
| C3 | 0.0374 (12) | 0.0491 (14) | 0.0536 (16) | −0.0082 (11) | −0.0061 (11) | 0.0061 (12) |
| C4 | 0.0438 (13) | 0.0377 (12) | 0.0466 (15) | −0.0035 (11) | 0.0052 (11) | 0.0043 (10) |
| C5 | 0.0372 (12) | 0.0410 (13) | 0.0453 (15) | 0.0003 (10) | 0.0036 (10) | 0.0056 (10) |
| C6 | 0.0454 (13) | 0.0421 (13) | 0.0496 (16) | −0.0006 (11) | −0.0025 (11) | 0.0073 (11) |
| C7 | 0.0763 (19) | 0.0634 (17) | 0.0583 (19) | 0.0160 (15) | −0.0215 (15) | −0.0017 (14) |
| C8 | 0.0493 (15) | 0.0527 (15) | 0.0471 (16) | 0.0037 (13) | 0.0046 (12) | 0.0088 (12) |
| C9 | 0.061 (2) | 0.103 (3) | 0.100 (3) | 0.0384 (19) | 0.0100 (18) | 0.008 (2) |
| C10 | 0.0468 (19) | 0.139 (4) | 0.196 (6) | 0.024 (2) | 0.007 (2) | 0.025 (4) |
| C11 | 0.0652 (17) | 0.0544 (16) | 0.0607 (19) | 0.0094 (13) | 0.0206 (14) | 0.0102 (13) |
| C12 | 0.074 (2) | 0.0620 (19) | 0.091 (3) | −0.0053 (16) | 0.0256 (19) | 0.0133 (17) |
| C13 | 0.083 (2) | 0.088 (2) | 0.110 (3) | −0.023 (2) | 0.007 (2) | −0.003 (2) |
| C14 | 0.102 (2) | 0.081 (2) | 0.056 (2) | 0.008 (2) | 0.0207 (18) | 0.0155 (17) |
| C15 | 0.135 (4) | 0.099 (3) | 0.071 (3) | 0.005 (2) | 0.001 (2) | −0.009 (2) |
| S1—O2 | 1.4183 (19) | C12—C13 | 1.504 (5) |
| S1—O3 | 1.4097 (19) | C14—C15 | 1.503 (5) |
| S1—N3 | 1.678 (2) | C3—H3A | 0.9700 |
| S1—N4 | 1.589 (2) | C3—H3B | 0.9700 |
| O1—N2 | 1.413 (3) | C4—H4 | 0.9300 |
| O1—C1 | 1.343 (3) | C7—H7A | 0.9600 |
| O4—C8 | 1.205 (3) | C7—H7B | 0.9600 |
| O5—C8 | 1.327 (3) | C7—H7C | 0.9600 |
| O5—C9 | 1.458 (3) | C9—H9A | 0.9700 |
| N1—C1 | 1.283 (3) | C9—H9B | 0.9700 |
| N1—C2 | 1.373 (3) | C10—H10A | 0.9600 |
| N2—C2 | 1.291 (3) | C10—H10B | 0.9600 |
| N3—C3 | 1.476 (3) | C10—H10C | 0.9600 |
| N3—C4 | 1.344 (3) | C11—H11 | 0.9800 |
| N4—C6 | 1.313 (3) | C12—H12A | 0.9700 |
| C1—C11 | 1.492 (4) | C12—H12B | 0.9700 |
| C2—C3 | 1.494 (3) | C13—H13A | 0.9600 |
| C4—C5 | 1.361 (3) | C13—H13B | 0.9600 |
| C5—C6 | 1.425 (3) | C13—H13C | 0.9600 |
| C5—C8 | 1.487 (3) | C14—H14A | 0.9700 |
| C6—C7 | 1.497 (3) | C14—H14B | 0.9700 |
| C9—C10 | 1.439 (5) | C15—H15A | 0.9600 |
| C11—C12 | 1.539 (4) | C15—H15B | 0.9600 |
| C11—C14 | 1.518 (4) | C15—H15C | 0.9600 |
| O2—S1—N3 | 107.26 (11) | N2—C2—C3 | 120.9 (2) |
| O2—S1—N4 | 110.56 (11) | N3—C3—C2 | 110.41 (18) |
| O3—S1—O2 | 116.64 (13) | N3—C4—C5 | 124.0 (2) |
| O3—S1—N3 | 106.67 (11) | C4—C5—C6 | 119.7 (2) |
| O3—S1—N4 | 111.17 (13) | C4—C5—C8 | 114.5 (2) |
| N4—S1—N3 | 103.55 (10) | C6—C5—C8 | 125.5 (2) |
| C1—O1—N2 | 106.41 (17) | N4—C6—C5 | 122.6 (2) |
| C8—O5—C9 | 116.2 (2) | N4—C6—C7 | 114.7 (2) |
| C1—N1—C2 | 102.8 (2) | C5—C6—C7 | 122.6 (2) |
| C2—N2—O1 | 102.71 (18) | O4—C8—O5 | 124.6 (2) |
| C3—N3—S1 | 118.03 (15) | O4—C8—C5 | 123.6 (2) |
| C4—N3—S1 | 118.60 (16) | O5—C8—C5 | 111.6 (2) |
| C4—N3—C3 | 121.5 (2) | C10—C9—O5 | 108.1 (3) |
| C6—N4—S1 | 122.23 (18) | C1—C11—C12 | 109.3 (2) |
| O1—C1—C11 | 116.3 (2) | C1—C11—C14 | 111.5 (2) |
| N1—C1—O1 | 112.9 (2) | C14—C11—C12 | 112.0 (3) |
| N1—C1—C11 | 130.7 (2) | C13—C12—C11 | 114.8 (3) |
| N1—C2—C3 | 123.9 (2) | C15—C14—C11 | 114.4 (3) |
| N2—C2—N1 | 115.1 (2) | ||
| S1—N3—C3—C2 | −71.7 (2) | N4—S1—N3—C4 | 31.0 (2) |
| S1—N3—C4—C5 | −14.3 (3) | C1—O1—N2—C2 | 0.6 (3) |
| S1—N4—C6—C5 | 13.9 (3) | C1—N1—C2—N2 | −0.9 (3) |
| S1—N4—C6—C7 | −171.32 (19) | C1—N1—C2—C3 | 176.3 (2) |
| O1—N2—C2—N1 | 0.2 (3) | C1—C11—C12—C13 | −62.4 (3) |
| O1—N2—C2—C3 | −177.1 (2) | C1—C11—C14—C15 | 61.6 (4) |
| O1—C1—C11—C12 | −66.6 (3) | C2—N1—C1—O1 | 1.4 (3) |
| O1—C1—C11—C14 | 57.8 (3) | C2—N1—C1—C11 | −175.8 (3) |
| O2—S1—N3—C3 | 78.61 (19) | C3—N3—C4—C5 | −178.3 (2) |
| O2—S1—N3—C4 | −85.95 (19) | C4—N3—C3—C2 | 92.4 (3) |
| O2—S1—N4—C6 | 83.5 (2) | C4—C5—C6—N4 | 9.6 (4) |
| O3—S1—N3—C3 | −47.1 (2) | C4—C5—C6—C7 | −164.7 (2) |
| O3—S1—N3—C4 | 148.37 (19) | C4—C5—C8—O4 | 23.7 (4) |
| O3—S1—N4—C6 | −145.3 (2) | C4—C5—C8—O5 | −152.6 (2) |
| N1—C1—C11—C12 | 110.4 (3) | C6—C5—C8—O4 | −149.2 (3) |
| N1—C1—C11—C14 | −125.2 (3) | C6—C5—C8—O5 | 34.4 (3) |
| N1—C2—C3—N3 | −50.0 (3) | C8—O5—C9—C10 | −166.0 (3) |
| N2—O1—C1—N1 | −1.3 (3) | C8—C5—C6—N4 | −177.8 (2) |
| N2—O1—C1—C11 | 176.3 (2) | C8—C5—C6—C7 | 7.9 (4) |
| N2—C2—C3—N3 | 127.1 (2) | C9—O5—C8—O4 | 2.1 (4) |
| N3—S1—N4—C6 | −31.1 (2) | C9—O5—C8—C5 | 178.4 (2) |
| N3—C4—C5—C6 | −8.5 (4) | C12—C11—C14—C15 | −175.5 (3) |
| N3—C4—C5—C8 | 178.1 (2) | C14—C11—C12—C13 | 173.4 (3) |
| N4—S1—N3—C3 | −164.45 (17) |
| H··· | ||||
| C4—H4···N2i | 0.93 | 2.54 | 3.431 (3) | 161 |