data_3IN3 # _model_server_result.job_id hm4mvfnNSILIR3JusbaVEw _model_server_result.datetime_utc '2025-01-21 04:56:26' _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 3in3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3IN3 # _exptl.entry_id 3IN3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 343.382 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5S)-2-amino-3-methyl-5-pyridin-4-yl-5-(3-pyridin-3-ylphenyl)-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 94.79 _cell.angle_gamma 90 _cell.entry_id 3IN3 _cell.length_a 73.379 _cell.length_b 104.854 _cell.length_c 50.531 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IN3 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 233 A CYS 279 1_555 A SG CYS 398 A CYS 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 A SG CYS 285 A CYS 331 1_555 A SG CYS 335 A CYS 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _chem_comp.formula 'C20 H17 N5 O' _chem_comp.formula_weight 343.382 _chem_comp.id 472 _chem_comp.mon_nstd_flag . _chem_comp.name (5S)-2-amino-3-methyl-5-pyridin-4-yl-5-(3-pyridin-3-ylphenyl)-3,5-dihydro-4H-imidazol-4-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N1 C1 472 sing 1 n n C1 H1 472 sing 2 n n C1 H1A 472 sing 3 n n C1 H1B 472 sing 4 n n C4 N1 472 sing 5 n n N1 C2 472 sing 6 n n C2 O1 472 doub 7 n n C3 C2 472 sing 8 n n N2 C4 472 doub 9 n n N2 C3 472 sing 10 n n C10 C3 472 sing 11 n n C3 C5 472 sing 12 n n N3 C4 472 sing 13 n n N3 HN3 472 sing 14 n n N3 HN3A 472 sing 15 n n C7 N4 472 doub 16 n y N4 C8 472 sing 17 n y C6 C5 472 doub 18 n y C5 C9 472 sing 19 n y N5 C20 472 doub 20 n y N5 C19 472 sing 21 n y C6 C7 472 sing 22 n y C6 H6 472 sing 23 n n C7 H7 472 sing 24 n n C9 C8 472 doub 25 n y C8 H8 472 sing 26 n n C9 H9 472 sing 27 n n C15 C10 472 doub 28 n y C10 C11 472 sing 29 n y C12 C11 472 doub 30 n y C11 H11 472 sing 31 n n C13 C12 472 sing 32 n y C12 H12 472 sing 33 n n C14 C13 472 doub 34 n y C13 H13 472 sing 35 n n C16 C14 472 sing 36 n y C14 C15 472 sing 37 n y C15 H15 472 sing 38 n n C20 C16 472 sing 39 n y C16 C17 472 doub 40 n y C18 C17 472 sing 41 n y C17 H17 472 sing 42 n n C19 C18 472 doub 43 n y C18 H18 472 sing 44 n n C19 H19 472 sing 45 n n C20 H20 472 sing 46 n n # _atom_sites.entry_id 3IN3 _atom_sites.fract_transf_matrix[1][1] 0.013628 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001142 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009537 _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] 0.019859 _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 2 472 A 1 1 1 472 472 . 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 1 HOH HOH . C 3 HOH A 47 463 47 HOH HOH . C 3 HOH A 48 464 48 HOH HOH . C 3 HOH A 49 465 49 HOH HOH . C 3 HOH A 50 466 50 HOH HOH . C 3 HOH A 51 467 51 HOH HOH . C 3 HOH A 52 468 52 HOH HOH . C 3 HOH A 53 469 54 HOH HOH . C 3 HOH A 54 470 55 HOH HOH . C 3 HOH A 55 471 56 HOH HOH . C 3 HOH A 56 472 57 HOH HOH . C 3 HOH A 57 473 58 HOH HOH . C 3 HOH A 58 474 59 HOH HOH . C 3 HOH A 59 475 60 HOH HOH . C 3 HOH A 60 476 61 HOH HOH . C 3 HOH A 61 477 62 HOH HOH . C 3 HOH A 62 478 63 HOH HOH . C 3 HOH A 63 479 64 HOH HOH . C 3 HOH A 64 480 65 HOH HOH . C 3 HOH A 65 481 66 HOH HOH . C 3 HOH A 66 482 67 HOH HOH . C 3 HOH A 67 483 68 HOH HOH . C 3 HOH A 68 484 69 HOH HOH . C 3 HOH A 69 485 70 HOH HOH . C 3 HOH A 70 486 72 HOH HOH . C 3 HOH A 71 487 73 HOH HOH . C 3 HOH A 72 488 74 HOH HOH . C 3 HOH A 73 489 75 HOH HOH . C 3 HOH A 74 490 76 HOH HOH . C 3 HOH A 75 491 77 HOH HOH . C 3 HOH A 76 492 79 HOH HOH . C 3 HOH A 77 493 80 HOH HOH . C 3 HOH A 78 494 81 HOH HOH . C 3 HOH A 79 495 82 HOH HOH . C 3 HOH A 80 496 83 HOH HOH . C 3 HOH A 81 497 84 HOH HOH . C 3 HOH A 82 498 85 HOH HOH . C 3 HOH A 83 499 86 HOH HOH . C 3 HOH A 84 500 88 HOH HOH . C 3 HOH A 85 501 89 HOH HOH . C 3 HOH A 86 502 90 HOH HOH . C 3 HOH A 87 503 91 HOH HOH . C 3 HOH A 88 504 92 HOH HOH . C 3 HOH A 89 505 93 HOH HOH . C 3 HOH A 90 506 94 HOH HOH . C 3 HOH A 91 507 95 HOH HOH . C 3 HOH A 92 508 97 HOH HOH . C 3 HOH A 93 509 98 HOH HOH . C 3 HOH A 94 510 99 HOH HOH . C 3 HOH A 95 511 100 HOH HOH . C 3 HOH A 96 512 101 HOH HOH . C 3 HOH A 97 513 102 HOH HOH . C 3 HOH A 98 514 103 HOH HOH . C 3 HOH A 99 515 104 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 472 . . . B 2 15.972 -4.325 17.675 1 20.87 ? C1 472 1 A 1 HETATM 2 N N1 472 . . . B 2 15.402 -5.495 17.042 1 21.43 ? N1 472 1 A 1 HETATM 3 O O1 472 . . . B 2 14.344 -6.344 18.889 1 21.18 ? O1 472 1 A 1 HETATM 4 C C2 472 . . . B 2 14.642 -6.405 17.705 1 20.38 ? C2 472 1 A 1 HETATM 5 N N2 472 . . . B 2 14.91 -6.979 15.43 1 16.83 ? N2 472 1 A 1 HETATM 6 C C3 472 . . . B 2 14.219 -7.483 16.671 1 19.85 ? C3 472 1 A 1 HETATM 7 N N3 472 . . . B 2 16.324 -5.243 14.88 1 16.54 ? N3 472 1 A 1 HETATM 8 C C4 472 . . . B 2 15.51 -5.879 15.754 1 20.23 ? C4 472 1 A 1 HETATM 9 N N4 472 . . . B 2 15.707 -11.517 17.418 1 27.5 ? N4 472 1 A 1 HETATM 10 C C5 472 . . . B 2 14.743 -8.899 16.968 1 16.6 ? C5 472 1 A 1 HETATM 11 N N5 472 . . . B 2 9.98 -3.048 13.952 1 22.46 ? N5 472 1 A 1 HETATM 12 C C6 472 . . . B 2 15.012 -9.776 15.902 1 17.72 ? C6 472 1 A 1 HETATM 13 C C7 472 . . . B 2 15.485 -11.051 16.17 1 20.42 ? C7 472 1 A 1 HETATM 14 C C8 472 . . . B 2 15.448 -10.67 18.434 1 25.83 ? C8 472 1 A 1 HETATM 15 C C9 472 . . . B 2 14.972 -9.373 18.266 1 28.27 ? C9 472 1 A 1 HETATM 16 C C10 472 . . . B 2 12.679 -7.441 16.563 1 20.47 ? C10 472 1 A 1 HETATM 17 C C11 472 . . . B 2 11.86 -8.539 16.883 1 23.18 ? C11 472 1 A 1 HETATM 18 C C12 472 . . . B 2 10.471 -8.445 16.769 1 24.72 ? C12 472 1 A 1 HETATM 19 C C13 472 . . . B 2 9.869 -7.26 16.337 1 21.42 ? C13 472 1 A 1 HETATM 20 C C14 472 . . . B 2 10.653 -6.145 16.01 1 23.56 ? C14 472 1 A 1 HETATM 21 C C15 472 . . . B 2 12.048 -6.261 16.132 1 21.18 ? C15 472 1 A 1 HETATM 22 C C16 472 . . . B 2 10.061 -4.876 15.563 1 21.72 ? C16 472 1 A 1 HETATM 23 C C17 472 . . . B 2 9.03 -4.253 16.282 1 21.03 ? C17 472 1 A 1 HETATM 24 C C18 472 . . . B 2 8.483 -3.049 15.841 1 22.98 ? C18 472 1 A 1 HETATM 25 C C19 472 . . . B 2 8.986 -2.486 14.679 1 19.43 ? C19 472 1 A 1 HETATM 26 C C20 472 . . . B 2 10.491 -4.221 14.41 1 14.95 ? C20 472 1 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #