data_3S7M # _model_server_result.job_id BprTBhG8P7B8FMe4S46yoQ _model_server_result.datetime_utc '2025-01-21 05:01:53' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3s7m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3S7M # _exptl.entry_id 3S7M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 348.422 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5S)-2-amino-3-methyl-5-[3-(pyridin-3-yl)phenyl]-5-(thiophen-3-yl)-3,5-dihydro-4H-imidazol-4-one _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.9 _cell.angle_gamma 90 _cell.entry_id 3S7M _cell.length_a 72.389 _cell.length_b 103.979 _cell.length_c 50.137 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S7M _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 171 A CYS 217 1_555 A SG CYS 375 A CYS 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 233 A CYS 279 1_555 A SG CYS 398 A CYS 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 285 A CYS 331 1_555 A SG CYS 335 A CYS 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? # _chem_comp.formula 'C19 H16 N4 O S' _chem_comp.formula_weight 348.422 _chem_comp.id 532 _chem_comp.mon_nstd_flag . _chem_comp.name (5S)-2-amino-3-methyl-5-[3-(pyridin-3-yl)phenyl]-5-(thiophen-3-yl)-3,5-dihydro-4H-imidazol-4-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms WAY-253284 # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 N1 532 sing 1 n n N1 C2 532 sing 2 n n N1 C4 532 sing 3 n n O1 C2 532 doub 4 n n S1 C18 532 sing 5 n y S1 C19 532 sing 6 n y C2 C3 532 sing 7 n n N2 C3 532 sing 8 n n N2 C4 532 doub 9 n n C3 C5 532 sing 10 n n C3 C16 532 sing 11 n n N3 C4 532 sing 12 n n N4 C14 532 doub 13 n y N4 C15 532 sing 14 n y C5 C6 532 doub 15 n y C5 C10 532 sing 16 n y C6 C7 532 sing 17 n y C7 C8 532 doub 18 n y C8 C9 532 sing 19 n y C9 C10 532 doub 20 n y C9 C11 532 sing 21 n y C11 C12 532 sing 22 n y C11 C15 532 doub 23 n y C12 C13 532 doub 24 n y C13 C14 532 sing 25 n y C16 C17 532 sing 26 n y C16 C19 532 doub 27 n y C17 C18 532 doub 28 n y C1 H1 532 sing 29 n n C1 H1A 532 sing 30 n n C1 H1B 532 sing 31 n n N3 HN3 532 sing 32 n n N3 HN3A 532 sing 33 n n C6 H6 532 sing 34 n n C7 H7 532 sing 35 n n C8 H8 532 sing 36 n n C10 H10 532 sing 37 n n C12 H12 532 sing 38 n n C13 H13 532 sing 39 n n C14 H14 532 sing 40 n n C15 H15 532 sing 41 n n C17 H17 532 sing 42 n n C18 H18 532 sing 43 n n C19 H19 532 sing 44 n n # _atom_sites.entry_id 3S7M _atom_sites.fract_transf_matrix[1][1] 0.013814 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001184 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009617 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.020019 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 532 A 1 1 1 532 532 . C 3 HOH A 1 2 2 HOH HOH . C 3 HOH A 2 3 3 HOH HOH . C 3 HOH A 3 4 4 HOH HOH . C 3 HOH A 4 5 5 HOH HOH . C 3 HOH A 5 6 6 HOH HOH . C 3 HOH A 6 7 7 HOH HOH . C 3 HOH A 7 8 8 HOH HOH . C 3 HOH A 8 9 9 HOH HOH . C 3 HOH A 9 10 10 HOH HOH . C 3 HOH A 10 11 11 HOH HOH . C 3 HOH A 11 12 12 HOH HOH . C 3 HOH A 12 13 13 HOH HOH . C 3 HOH A 13 14 14 HOH HOH . C 3 HOH A 14 15 15 HOH HOH . C 3 HOH A 15 16 16 HOH HOH . C 3 HOH A 16 17 17 HOH HOH . C 3 HOH A 17 18 18 HOH HOH . C 3 HOH A 18 19 19 HOH HOH . C 3 HOH A 19 20 20 HOH HOH . C 3 HOH A 20 21 21 HOH HOH . C 3 HOH A 21 22 22 HOH HOH . C 3 HOH A 22 23 23 HOH HOH . C 3 HOH A 23 24 24 HOH HOH . C 3 HOH A 24 25 25 HOH HOH . C 3 HOH A 25 26 26 HOH HOH . C 3 HOH A 26 27 27 HOH HOH . C 3 HOH A 27 28 28 HOH HOH . C 3 HOH A 28 29 29 HOH HOH . C 3 HOH A 29 30 30 HOH HOH . C 3 HOH A 30 31 31 HOH HOH . C 3 HOH A 31 32 32 HOH HOH . C 3 HOH A 32 33 33 HOH HOH . C 3 HOH A 33 34 34 HOH HOH . C 3 HOH A 34 35 35 HOH HOH . C 3 HOH A 35 36 36 HOH HOH . C 3 HOH A 36 37 37 HOH HOH . C 3 HOH A 37 38 38 HOH HOH . C 3 HOH A 38 39 39 HOH HOH . C 3 HOH A 39 40 40 HOH HOH . C 3 HOH A 40 41 41 HOH HOH . C 3 HOH A 41 42 42 HOH HOH . C 3 HOH A 42 43 43 HOH HOH . C 3 HOH A 43 44 44 HOH HOH . C 3 HOH A 44 45 45 HOH HOH . C 3 HOH A 45 46 46 HOH HOH . C 3 HOH A 46 462 462 HOH HOH . C 3 HOH A 47 463 463 HOH HOH . C 3 HOH A 48 464 464 HOH HOH . C 3 HOH A 49 465 465 HOH HOH . C 3 HOH A 50 466 466 HOH HOH . C 3 HOH A 51 467 467 HOH HOH . C 3 HOH A 52 468 468 HOH HOH . C 3 HOH A 53 469 469 HOH HOH . C 3 HOH A 54 470 470 HOH HOH . C 3 HOH A 55 471 471 HOH HOH . C 3 HOH A 56 472 472 HOH HOH . C 3 HOH A 57 473 473 HOH HOH . C 3 HOH A 58 474 474 HOH HOH . C 3 HOH A 59 475 475 HOH HOH . C 3 HOH A 60 476 476 HOH HOH . C 3 HOH A 61 477 477 HOH HOH . C 3 HOH A 62 478 478 HOH HOH . C 3 HOH A 63 479 479 HOH HOH . C 3 HOH A 64 480 480 HOH HOH . C 3 HOH A 65 481 481 HOH HOH . C 3 HOH A 66 482 482 HOH HOH . C 3 HOH A 67 483 483 HOH HOH . C 3 HOH A 68 484 484 HOH HOH . C 3 HOH A 69 485 485 HOH HOH . C 3 HOH A 70 486 486 HOH HOH . C 3 HOH A 71 487 487 HOH HOH . C 3 HOH A 72 488 488 HOH HOH . C 3 HOH A 73 489 489 HOH HOH . C 3 HOH A 74 490 490 HOH HOH . C 3 HOH A 75 491 491 HOH HOH . C 3 HOH A 76 492 492 HOH HOH . C 3 HOH A 77 493 493 HOH HOH . C 3 HOH A 78 494 494 HOH HOH . C 3 HOH A 79 495 495 HOH HOH . C 3 HOH A 80 496 496 HOH HOH . C 3 HOH A 81 497 497 HOH HOH . C 3 HOH A 82 498 498 HOH HOH . C 3 HOH A 83 499 499 HOH HOH . C 3 HOH A 84 500 500 HOH HOH . C 3 HOH A 85 501 501 HOH HOH . C 3 HOH A 86 502 502 HOH HOH . C 3 HOH A 87 503 503 HOH HOH . C 3 HOH A 88 504 504 HOH HOH . C 3 HOH A 89 505 505 HOH HOH . C 3 HOH A 90 506 506 HOH HOH . C 3 HOH A 91 507 507 HOH HOH . C 3 HOH A 92 508 508 HOH HOH . C 3 HOH A 93 509 509 HOH HOH . C 3 HOH A 94 510 510 HOH HOH . C 3 HOH A 95 511 511 HOH HOH . C 3 HOH A 96 512 512 HOH HOH . C 3 HOH A 97 513 513 HOH HOH . C 3 HOH A 98 514 514 HOH HOH . C 3 HOH A 99 515 515 HOH HOH . C 3 HOH A 100 516 516 HOH HOH . C 3 HOH A 101 517 517 HOH HOH . C 3 HOH A 102 518 518 HOH HOH . C 3 HOH A 103 519 519 HOH HOH . C 3 HOH A 104 520 520 HOH HOH . C 3 HOH A 105 521 521 HOH HOH . C 3 HOH A 106 522 522 HOH HOH . C 3 HOH A 107 523 523 HOH HOH . C 3 HOH A 108 524 524 HOH HOH . C 3 HOH A 109 525 525 HOH HOH . C 3 HOH A 110 526 526 HOH HOH . C 3 HOH A 111 527 527 HOH HOH . C 3 HOH A 112 528 528 HOH HOH . C 3 HOH A 113 529 529 HOH HOH . C 3 HOH A 114 530 530 HOH HOH . C 3 HOH A 115 531 531 HOH HOH . C 3 HOH A 116 532 532 HOH HOH . C 3 HOH A 117 533 533 HOH HOH . C 3 HOH A 118 534 534 HOH HOH . C 3 HOH A 119 535 535 HOH HOH . C 3 HOH A 120 536 536 HOH HOH . C 3 HOH A 121 537 537 HOH HOH . C 3 HOH A 122 538 538 HOH HOH . C 3 HOH A 123 539 539 HOH HOH . C 3 HOH A 124 540 540 HOH HOH . C 3 HOH A 125 541 541 HOH HOH . C 3 HOH A 126 542 542 HOH HOH . C 3 HOH A 127 543 543 HOH HOH . C 3 HOH A 128 544 544 HOH HOH . C 3 HOH A 129 545 545 HOH HOH . C 3 HOH A 130 546 546 HOH HOH . C 3 HOH A 131 547 547 HOH HOH . C 3 HOH A 132 548 548 HOH HOH . C 3 HOH A 133 549 549 HOH HOH . C 3 HOH A 134 550 550 HOH HOH . C 3 HOH A 135 551 551 HOH HOH . C 3 HOH A 136 552 552 HOH HOH . C 3 HOH A 137 553 553 HOH HOH . C 3 HOH A 138 554 554 HOH HOH . C 3 HOH A 139 555 555 HOH HOH . C 3 HOH A 140 556 556 HOH HOH . C 3 HOH A 141 557 557 HOH HOH . C 3 HOH A 142 558 558 HOH HOH . C 3 HOH A 143 559 559 HOH HOH . C 3 HOH A 144 560 560 HOH HOH . C 3 HOH A 145 561 561 HOH HOH . C 3 HOH A 146 562 562 HOH HOH . C 3 HOH A 147 563 563 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 532 . . . B 2 15.556 -4.112 17.541 1 11.02 ? C1 532 1 A 1 HETATM 2 N N1 532 . . . B 2 15.071 -5.319 16.931 1 14.98 ? N1 532 1 A 1 HETATM 3 O O1 532 . . . B 2 13.915 -6.108 18.749 1 17.88 ? O1 532 1 A 1 HETATM 4 S S1 532 . . . B 2 15.289 -10.687 18.36 1 23.98 ? S1 532 1 A 1 HETATM 5 C C2 532 . . . B 2 14.303 -6.206 17.586 1 15.12 ? C2 532 1 A 1 HETATM 6 N N2 532 . . . B 2 14.686 -6.816 15.311 1 15.03 ? N2 532 1 A 1 HETATM 7 C C3 532 . . . B 2 13.999 -7.291 16.554 1 15.91 ? C3 532 1 A 1 HETATM 8 N N3 532 . . . B 2 16.101 -5.064 14.878 1 13.19 ? N3 532 1 A 1 HETATM 9 C C4 532 . . . B 2 15.262 -5.73 15.672 1 14.89 ? C4 532 1 A 1 HETATM 10 N N4 532 . . . B 2 9.995 -2.965 13.762 1 17.65 ? N4 532 1 A 1 HETATM 11 C C5 532 . . . B 2 12.482 -7.379 16.446 1 13.81 ? C5 532 1 A 1 HETATM 12 C C6 532 . . . B 2 11.702 -8.489 16.785 1 19.33 ? C6 532 1 A 1 HETATM 13 C C7 532 . . . B 2 10.313 -8.416 16.635 1 23.83 ? C7 532 1 A 1 HETATM 14 C C8 532 . . . B 2 9.684 -7.265 16.169 1 13.52 ? C8 532 1 A 1 HETATM 15 C C9 532 . . . B 2 10.452 -6.141 15.818 1 19.87 ? C9 532 1 A 1 HETATM 16 C C10 532 . . . B 2 11.833 -6.25 15.983 1 11.87 ? C10 532 1 A 1 HETATM 17 C C11 532 . . . B 2 9.893 -4.858 15.329 1 14.29 ? C11 532 1 A 1 HETATM 18 C C12 532 . . . B 2 8.757 -4.271 15.914 1 15.07 ? C12 532 1 A 1 HETATM 19 C C13 532 . . . B 2 8.264 -3.064 15.425 1 22.83 ? C13 532 1 A 1 HETATM 20 C C14 532 . . . B 2 8.911 -2.447 14.353 1 12.62 ? C14 532 1 A 1 HETATM 21 C C15 532 . . . B 2 10.452 -4.145 14.264 1 15.17 ? C15 532 1 A 1 HETATM 22 C C16 532 . . . B 2 14.521 -8.64 16.957 1 9.47 ? C16 532 1 A 1 HETATM 23 C C17 532 . . . B 2 14.95 -9.631 16.028 1 15.03 ? C17 532 1 A 1 HETATM 24 C C18 532 . . . B 2 15.383 -10.772 16.659 1 13.42 ? C18 532 1 A 1 HETATM 25 C C19 532 . . . B 2 14.662 -9.095 18.25 1 19.06 ? C19 532 1 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #