data_4D9 # _chem_comp.id 4D9 _chem_comp.name "3-(1H-benzimidazol-2-yl)-N-(1-benzothiophen-2-ylcarbonyl)-D-alanine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H15 N3 O3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(R)-2-[(Benzo[b]thiophene-2-carbonyl)-amino]-3-(1H-benzoimidazol-2-yl)-propionic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-10-22 _chem_comp.pdbx_modified_date 2020-06-17 _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 365.406 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 4D9 _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 3KAF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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.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 4D9 C1 C1 C 0 1 Y N N 39.425 -18.644 13.843 -5.006 2.479 -0.437 C1 4D9 1 4D9 C2 C2 C 0 1 Y N N 39.592 -20.011 13.663 -4.567 3.782 -0.551 C2 4D9 2 4D9 C3 C3 C 0 1 Y N N 39.395 -20.572 12.398 -3.239 4.100 -0.306 C3 4D9 3 4D9 C4 C4 C 0 1 Y N N 39.044 -19.819 11.272 -2.345 3.131 0.052 C4 4D9 4 4D9 N5 N5 N 0 1 Y N N 38.848 -16.537 12.612 -4.222 0.121 0.135 N5 4D9 5 4D9 C6 C6 C 0 1 Y N N 39.075 -17.842 12.762 -4.114 1.482 -0.069 C6 4D9 6 4D9 C7 C7 C 0 1 Y N N 38.881 -18.458 11.431 -2.767 1.804 0.173 C7 4D9 7 4D9 N8 N8 N 0 1 Y N N 38.554 -17.461 10.615 -2.137 0.647 0.502 N8 4D9 8 4D9 C9 C9 C 0 1 Y N N 38.537 -16.302 11.327 -2.987 -0.337 0.473 C9 4D9 9 4D9 C10 C10 C 0 1 N N N 38.223 -14.944 10.732 -2.654 -1.774 0.782 C10 4D9 10 4D9 C11 C11 C 0 1 N N R 39.459 -14.065 10.447 -1.500 -2.234 -0.112 C11 4D9 11 4D9 C12 C12 C 0 1 N N N 38.988 -12.768 9.820 -1.249 -3.703 0.109 C12 4D9 12 4D9 N13 N13 N 0 1 N N N 40.563 -14.625 9.661 -0.292 -1.476 0.222 N13 4D9 13 4D9 O14 O14 O 0 1 N N N 38.725 -12.723 8.582 -0.171 -4.079 0.505 O14 4D9 14 4D9 O15 O15 O 0 1 N N N 38.870 -11.770 10.582 -2.222 -4.595 -0.134 O15 4D9 15 4D9 C16 C16 C 0 1 N N N 40.811 -15.895 9.280 0.679 -1.316 -0.698 C16 4D9 16 4D9 C17 C17 C 0 1 Y N N 40.564 -16.258 7.846 1.892 -0.555 -0.363 C17 4D9 17 4D9 O18 O18 O 0 1 N N N 41.242 -16.745 10.049 0.552 -1.801 -1.807 O18 4D9 18 4D9 C19 C19 C 0 1 Y N N 40.061 -15.457 6.799 2.910 -0.340 -1.202 C19 4D9 19 4D9 S20 S20 S 0 1 Y N N 40.932 -17.919 7.354 2.198 0.201 1.191 S20 4D9 20 4D9 C21 C21 C 0 1 Y N N 40.451 -17.643 5.751 3.758 0.805 0.646 C21 4D9 21 4D9 C22 C22 C 0 1 Y N N 39.991 -16.232 5.581 3.975 0.414 -0.682 C22 4D9 22 4D9 C23 C23 C 0 1 Y N N 39.544 -15.799 4.326 5.179 0.804 -1.315 C23 4D9 23 4D9 C24 C24 C 0 1 Y N N 39.544 -16.720 3.273 6.103 1.542 -0.644 C24 4D9 24 4D9 C25 C25 C 0 1 Y N N 39.987 -18.055 3.445 5.885 1.925 0.673 C25 4D9 25 4D9 C26 C26 C 0 1 Y N N 40.455 -18.541 4.678 4.723 1.565 1.314 C26 4D9 26 4D9 H1 H1 H 0 1 N N N 39.567 -18.205 14.820 -6.041 2.237 -0.629 H1 4D9 27 4D9 H2 H2 H 0 1 N N N 39.873 -20.638 14.497 -5.262 4.559 -0.834 H2 4D9 28 4D9 H3 H3 H 0 1 N N N 39.520 -21.639 12.284 -2.909 5.124 -0.399 H3 4D9 29 4D9 H4 H4 H 0 1 N N N 38.905 -20.288 10.309 -1.313 3.389 0.239 H4 4D9 30 4D9 H10 H10 H 0 1 N N N 37.700 -15.108 9.778 -2.361 -1.863 1.828 H10 4D9 31 4D9 H10A H10A H 0 0 N N N 37.584 -14.404 11.446 -3.529 -2.398 0.596 H10A 4D9 32 4D9 H11 H11 H 0 1 N N N 39.923 -13.941 11.437 -1.760 -2.063 -1.156 H11 4D9 33 4D9 HN13 HN13 H 0 0 N N N 41.243 -13.957 9.358 -0.191 -1.089 1.106 HN13 4D9 34 4D9 HO15 HO15 H 0 0 N N N 38.565 -11.023 10.081 -2.014 -5.526 0.022 HO15 4D9 35 4D9 H19 H19 H 0 1 N N N 39.772 -14.421 6.893 2.914 -0.720 -2.213 H19 4D9 36 4D9 H23 H23 H 0 1 N N N 39.209 -14.783 4.176 5.365 0.514 -2.338 H23 4D9 37 4D9 H24 H24 H 0 1 N N N 39.196 -16.404 2.300 7.017 1.832 -1.140 H24 4D9 38 4D9 H25 H25 H 0 1 N N N 39.964 -18.724 2.597 6.628 2.510 1.194 H25 4D9 39 4D9 H26 H26 H 0 1 N N N 40.801 -19.558 4.792 4.558 1.866 2.338 H26 4D9 40 4D9 HN5 HN5 H 0 1 N N N 38.901 -15.848 13.335 -5.028 -0.411 0.043 HN5 4D9 41 # # 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 4D9 C6 C1 DOUB Y N 1 4D9 C2 C1 SING Y N 2 4D9 C1 H1 SING N N 3 4D9 C3 C2 DOUB Y N 4 4D9 C2 H2 SING N N 5 4D9 C4 C3 SING Y N 6 4D9 C3 H3 SING N N 7 4D9 C4 C7 DOUB Y N 8 4D9 C4 H4 SING N N 9 4D9 C9 N5 SING Y N 10 4D9 N5 C6 SING Y N 11 4D9 C7 C6 SING Y N 12 4D9 N8 C7 SING Y N 13 4D9 N8 C9 DOUB Y N 14 4D9 C10 C9 SING N N 15 4D9 C11 C10 SING N N 16 4D9 C10 H10 SING N N 17 4D9 C10 H10A SING N N 18 4D9 N13 C11 SING N N 19 4D9 C12 C11 SING N N 20 4D9 C11 H11 SING N N 21 4D9 O14 C12 DOUB N N 22 4D9 C12 O15 SING N N 23 4D9 C16 N13 SING N N 24 4D9 N13 HN13 SING N N 25 4D9 O15 HO15 SING N N 26 4D9 C17 C16 SING N N 27 4D9 C16 O18 DOUB N N 28 4D9 C19 C17 DOUB Y N 29 4D9 S20 C17 SING Y N 30 4D9 C22 C19 SING Y N 31 4D9 C19 H19 SING N N 32 4D9 C21 S20 SING Y N 33 4D9 C26 C21 DOUB Y N 34 4D9 C22 C21 SING Y N 35 4D9 C23 C22 DOUB Y N 36 4D9 C24 C23 SING Y N 37 4D9 C23 H23 SING N N 38 4D9 C24 C25 DOUB Y N 39 4D9 C24 H24 SING N N 40 4D9 C25 C26 SING Y N 41 4D9 C25 H25 SING N N 42 4D9 C26 H26 SING N N 43 4D9 N5 HN5 SING N N 44 # # 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 4D9 SMILES ACDLabs 11.02 "O=C(O)C(NC(=O)c2sc1ccccc1c2)Cc4nc3ccccc3n4" 4D9 SMILES_CANONICAL CACTVS 3.352 "OC(=O)[C@@H](Cc1[nH]c2ccccc2n1)NC(=O)c3sc4ccccc4c3" 4D9 SMILES CACTVS 3.352 "OC(=O)[CH](Cc1[nH]c2ccccc2n1)NC(=O)c3sc4ccccc4c3" 4D9 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1ccc2c(c1)cc(s2)C(=O)N[C@H](Cc3[nH]c4ccccc4n3)C(=O)O" 4D9 SMILES "OpenEye OEToolkits" 1.7.0 "c1ccc2c(c1)cc(s2)C(=O)NC(Cc3[nH]c4ccccc4n3)C(=O)O" 4D9 InChI InChI 1.03 "InChI=1S/C19H15N3O3S/c23-18(16-9-11-5-1-4-8-15(11)26-16)22-14(19(24)25)10-17-20-12-6-2-3-7-13(12)21-17/h1-9,14H,10H2,(H,20,21)(H,22,23)(H,24,25)/t14-/m1/s1" 4D9 InChIKey InChI 1.03 OEMQUBXYMQNIGH-CQSZACIVSA-N # # 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 4D9 "SYSTEMATIC NAME" ACDLabs 11.02 "3-(1H-benzimidazol-2-yl)-N-(1-benzothiophen-2-ylcarbonyl)-D-alanine" 4D9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "(2R)-3-(1H-benzimidazol-2-yl)-2-(1-benzothiophen-2-ylcarbonylamino)propanoic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 4D9 "Create component" 2009-10-22 PDBJ 4D9 "Modify aromatic_flag" 2011-06-04 RCSB 4D9 "Modify descriptor" 2011-06-04 RCSB 4D9 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 4D9 _pdbx_chem_comp_synonyms.name "(R)-2-[(Benzo[b]thiophene-2-carbonyl)-amino]-3-(1H-benzoimidazol-2-yl)-propionic acid" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##