data_V8M
# 
_chem_comp.id                                    V8M 
_chem_comp.name                                  "N-[2-(2-hydroxy-5-nitrophenyl)ethyl]-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H24 N4 O5 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-07-17 
_chem_comp.pdbx_modified_date                    2026-04-06 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        408.472 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     V8M 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        6XND 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
V8M C10  C1  C 0  1 N N N N N N -23.325 10.147 -15.516 3.103  0.473  -1.000 C10  V8M 1  
V8M C13  C2  C 0  1 N N S N N N -20.289 11.483 -17.651 6.735  1.259  0.086  C13  V8M 2  
V8M C15  C3  C 0  1 N N N N N N -19.178 13.344 -17.551 7.413  -0.005 1.872  C15  V8M 3  
V8M C22  C4  C 0  1 Y N N N N N -29.049 4.456  -16.281 -6.368 0.438  -0.444 C22  V8M 4  
V8M C28  C5  C 0  1 Y N N N N N -27.704 2.213  -17.206 -7.030 -1.860 0.951  C28  V8M 5  
V8M C02  C6  C 0  1 Y N N N N N -27.103 3.075  -16.302 -5.841 -1.800 0.238  C02  V8M 6  
V8M C03  C7  C 0  1 Y N N N N N -27.783 4.183  -15.834 -5.512 -0.647 -0.461 C03  V8M 7  
V8M C04  C8  C 0  1 N N N N N N -27.115 5.162  -14.853 -4.222 -0.578 -1.237 C04  V8M 8  
V8M C05  C9  C 0  1 N N N N N N -26.473 6.252  -15.715 -3.066 -0.281 -0.279 C05  V8M 9  
V8M C07  C10 C 0  1 N N N N N N -25.994 8.678  -15.393 -0.653 0.037  -0.393 C07  V8M 10 
V8M C08  C11 C 0  1 N N N N N N -25.550 9.755  -14.387 0.637  0.106  -1.169 C08  V8M 11 
V8M C09  C12 C 0  1 N N N N N N -24.621 10.818 -15.018 1.793  0.403  -0.212 C09  V8M 12 
V8M C11  C13 C 0  1 N N N N N N -22.448 11.103 -16.345 4.259  0.769  -0.042 C11  V8M 13 
V8M C12  C14 C 0  1 N N S N N N -21.206 10.454 -16.681 5.568  0.839  -0.830 C12  V8M 14 
V8M C18  C15 C 0  1 N N R N N N -18.976 11.181 -17.440 8.041  0.535  -0.264 C18  V8M 15 
V8M C19  C16 C 0  1 N N N N N N -18.919 9.884  -16.299 7.875  -0.438 -1.447 C19  V8M 16 
V8M C23  C17 C 0  1 Y N N N N N -29.659 3.595  -17.184 -7.552 0.375  0.267  C23  V8M 17 
V8M C27  C18 C 0  1 Y N N N N N -28.983 2.467  -17.648 -7.882 -0.773 0.964  C27  V8M 18 
V8M N06  N1  N 0  1 N N N N N N -26.047 7.337  -14.853 -1.812 -0.214 -1.033 N06  V8M 19 
V8M N14  N2  N 0  1 N N N N N N -20.486 12.785 -17.770 6.448  0.830  1.464  N14  V8M 20 
V8M N16  N3  N 0  1 N N N N N N -18.227 12.254 -17.423 8.361  -0.229 0.952  N16  V8M 21 
V8M N24  N4  N 1  1 N N N N N N -30.997 3.924  -17.631 -8.467 1.538  0.283  N24  V8M 22 
V8M O01  O1  O 0  1 N N N N N N -25.811 2.824  -15.836 -5.001 -2.868 0.223  O01  V8M 23 
V8M O17  O2  O 0  1 N N N N N N -18.892 14.486 -17.540 7.427  -0.513 2.976  O17  V8M 24 
V8M O21  O3  O 0  1 N N N N N N -26.305 8.883  -16.538 -0.648 0.208  0.808  O21  V8M 25 
V8M O25  O4  O 0  1 N N N N N N -32.064 3.884  -16.728 -8.177 2.549  -0.330 O25  V8M 26 
V8M O26  O5  O -1 1 N N N N N N -31.176 4.256  -18.750 -9.510 1.484  0.910  O26  V8M 27 
V8M S20  S1  S 0  1 N N N N N N -20.083 10.372 -15.435 6.079  -0.835 -1.395 S20  V8M 28 
V8M H102 H1  H 0  0 N N N N N N -22.748 9.805  -14.645 3.279  -0.481 -1.497 H102 V8M 29 
V8M H101 H2  H 0  0 N N N N N N -23.593 9.282  -16.141 3.036  1.265  -1.745 H101 V8M 30 
V8M H131 H3  H 0  0 N N N N N N -20.498 11.080 -18.653 6.878  2.339  0.043  H131 V8M 31 
V8M H221 H4  H 0  0 N N N N N N -29.570 5.336  -15.933 -6.109 1.337  -0.984 H221 V8M 32 
V8M H281 H5  H 0  0 N N N N N N -27.170 1.344  -17.563 -7.289 -2.757 1.495  H281 V8M 33 
V8M H042 H6  H 0  0 N N N N N N -27.866 5.600  -14.180 -4.046 -1.531 -1.735 H042 V8M 34 
V8M H041 H7  H 0  0 N N N N N N -26.348 4.644  -14.259 -4.288 0.215  -1.982 H041 V8M 35 
V8M H052 H8  H 0  0 N N N N N N -25.603 5.839  -16.247 -3.242 0.672  0.219  H052 V8M 36 
V8M H051 H9  H 0  0 N N N N N N -27.206 6.626  -16.445 -3.000 -1.074 0.467  H051 V8M 37 
V8M H081 H10 H 0  0 N N N N N N -26.445 10.259 -13.994 0.813  -0.847 -1.667 H081 V8M 38 
V8M H082 H11 H 0  0 N N N N N N -25.013 9.265  -13.561 0.571  0.899  -1.915 H082 V8M 39 
V8M H091 H12 H 0  0 N N N N N N -24.372 11.579 -14.264 1.859  -0.390 0.534  H091 V8M 40 
V8M H092 H13 H 0  0 N N N N N N -25.134 11.295 -15.866 1.617  1.356  0.286  H092 V8M 41 
V8M H112 H14 H 0  0 N N N N N N -22.979 11.378 -17.269 4.083  1.722  0.456  H112 V8M 42 
V8M H111 H15 H 0  0 N N N N N N -22.240 12.010 -15.758 4.325  -0.023 0.703  H111 V8M 43 
V8M H121 H16 H 0  0 N N N N N N -21.324 9.472  -17.162 5.474  1.523  -1.674 H121 V8M 44 
V8M H181 H18 H 0  0 N N N N N N -18.678 10.658 -18.361 8.829  1.259  -0.473 H181 V8M 45 
V8M H191 H19 H 0  0 N N N N N N -17.968 9.846  -15.747 8.136  0.047  -2.387 H191 V8M 46 
V8M H192 H20 H 0  0 N N N N N N -19.115 8.905  -16.760 8.473  -1.337 -1.295 H192 V8M 47 
V8M H271 H22 H 0  0 N N N N N N -29.459 1.798  -18.349 -8.807 -0.819 1.519  H271 V8M 48 
V8M H061 H23 H 0  0 N N N N N N -25.794 7.161  -13.902 -1.816 -0.351 -1.994 H061 V8M 49 
V8M H141 H24 H 0  0 N N N N N N -21.340 13.267 -17.966 5.683  1.107  1.991  H141 V8M 50 
V8M H161 H25 H 0  0 N N N N N N -17.232 12.310 -17.341 9.134  -0.803 1.069  H161 V8M 51 
V8M H011 H26 H 0  0 N N N N N N -25.555 3.508  -15.228 -5.171 -3.492 -0.495 H011 V8M 52 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
V8M C10 C09  SING N N 1  
V8M C10 C11  SING N N 2  
V8M C13 C12  SING N N 3  
V8M C13 C18  SING N N 4  
V8M C13 N14  SING N N 5  
V8M C15 N14  SING N N 6  
V8M C15 N16  SING N N 7  
V8M C15 O17  DOUB N N 8  
V8M C22 C03  DOUB Y N 9  
V8M C22 C23  SING Y N 10 
V8M C28 C02  DOUB Y N 11 
V8M C28 C27  SING Y N 12 
V8M C02 C03  SING Y N 13 
V8M C02 O01  SING N N 14 
V8M C03 C04  SING N N 15 
V8M C04 C05  SING N N 16 
V8M C05 N06  SING N N 17 
V8M C07 C08  SING N N 18 
V8M C07 N06  SING N N 19 
V8M C07 O21  DOUB N N 20 
V8M C08 C09  SING N N 21 
V8M C11 C12  SING N N 22 
V8M C12 S20  SING N N 23 
V8M C18 N16  SING N N 24 
V8M C19 S20  SING N N 25 
V8M C23 C27  DOUB Y N 26 
V8M C23 N24  SING N N 27 
V8M N24 O25  DOUB N N 28 
V8M N24 O26  SING N N 29 
V8M C10 H102 SING N N 30 
V8M C10 H101 SING N N 31 
V8M C13 H131 SING N N 32 
V8M C22 H221 SING N N 33 
V8M C28 H281 SING N N 34 
V8M C04 H042 SING N N 35 
V8M C04 H041 SING N N 36 
V8M C05 H052 SING N N 37 
V8M C05 H051 SING N N 38 
V8M C08 H081 SING N N 39 
V8M C08 H082 SING N N 40 
V8M C09 H091 SING N N 41 
V8M C09 H092 SING N N 42 
V8M C11 H112 SING N N 43 
V8M C11 H111 SING N N 44 
V8M C12 H121 SING N N 45 
V8M C18 H181 SING N N 46 
V8M C19 H191 SING N N 47 
V8M C19 H192 SING N N 48 
V8M C27 H271 SING N N 49 
V8M N06 H061 SING N N 50 
V8M N14 H141 SING N N 51 
V8M N16 H161 SING N N 52 
V8M O01 H011 SING N N 53 
V8M C18 C19  SING N N 54 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
V8M SMILES           ACDLabs              14.52   "O=C1NC2C(CCCCC(=O)NCCc3cc(ccc3O)[N+]([O-])=O)SCC2N1"                                                                                                                                  
V8M InChI            InChI                1.06    "InChI=1S/C18H24N4O5S/c23-14-6-5-12(22(26)27)9-11(14)7-8-19-16(24)4-2-1-3-15-17-13(10-28-15)20-18(25)21-17/h5-6,9,13,15,17,23H,1-4,7-8,10H2,(H,19,24)(H2,20,21,25)/t13-,15-,17-/m0/s1" 
V8M InChIKey         InChI                1.06    GGNOUTGIVZKNRF-QRTARXTBSA-N                                                                                                                                                            
V8M SMILES_CANONICAL CACTVS               3.385   "Oc1ccc(cc1CCNC(=O)CCCC[C@@H]2SC[C@@H]3NC(=O)N[C@H]23)[N+]([O-])=O"                                                                                                                    
V8M SMILES           CACTVS               3.385   "Oc1ccc(cc1CCNC(=O)CCCC[CH]2SC[CH]3NC(=O)N[CH]23)[N+]([O-])=O"                                                                                                                         
V8M SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1cc(c(cc1[N+](=O)[O-])CCNC(=O)CCCC[C@H]2[C@@H]3[C@H](CS2)NC(=O)N3)O"                                                                                                                 
V8M SMILES           "OpenEye OEToolkits" 3.1.0.0 "c1cc(c(cc1[N+](=O)[O-])CCNC(=O)CCCCC2C3C(CS2)NC(=O)N3)O"                                                                                                                              
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
V8M "SYSTEMATIC NAME" ACDLabs              14.52   "N-[2-(2-hydroxy-5-nitrophenyl)ethyl]-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide"                                                
V8M "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[2-(5-nitro-2-oxidanyl-phenyl)ethyl]pentanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
V8M "Create component"   2020-07-17 RCSB 
V8M "Modify atom id"     2020-07-17 RCSB 
V8M "Initial release"    2021-03-03 RCSB 
V8M "Other modification" 2026-04-06 RCSB 
# 
