data_8FZ1 # _model_server_result.job_id xylt5uqJTJgBt5OgfVjFBQ _model_server_result.datetime_utc '2024-11-22 05:41:14' _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 8fz1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1403}' # _entry.id 8FZ1 # _exptl.entry_id 8FZ1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 399.445 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2P)-2-{3-[(2-amino-4,5-dimethylphenyl)carbamoyl]phenyl}-1H-benzimidazole-4-carboxamide _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 8FZ1 _cell.length_a 95.598 _cell.length_b 95.598 _cell.length_c 128.814 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FZ1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,I,J,K,S 1 1 B,D,L,M,N,O,P,Q,R,T 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 G N N ? 5 N N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C GLC 1 D 1 GLC A 1501 SUC 2 n C FRU 2 D 2 FRU A 1501 SUC 2 n D GLC 1 E 1 GLC B 1101 SUC 2 n D FRU 2 E 2 FRU B 1101 SUC # 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 104 A CYS 845 1_555 B SG CYS 104 B CYS 845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 C C1 GLC . D GLC 1 1_555 C O2 FRU . D FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale2 D C1 GLC . E GLC 1 1_555 D O2 FRU . E FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? # _chem_comp.formula 'C23 H21 N5 O2' _chem_comp.formula_weight 399.445 _chem_comp.id YVB _chem_comp.mon_nstd_flag . _chem_comp.name (2P)-2-{3-[(2-amino-4,5-dimethylphenyl)carbamoyl]phenyl}-1H-benzimidazole-4-carboxamide _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 N4 C21 YVB sing 462 n n C21 C22 YVB doub 463 n y C21 C5 YVB sing 464 n y C22 C1 YVB sing 465 n y N C5 YVB sing 466 n n N C6 YVB sing 467 n n C5 C4 YVB doub 468 n y C12 C11 YVB doub 469 n y C12 C7 YVB sing 470 n y C11 C10 YVB sing 471 n y C1 C YVB sing 472 n n C1 C2 YVB doub 473 n y C4 C2 YVB sing 474 n y C2 C3 YVB sing 475 n n C7 C6 YVB sing 476 n n C7 C8 YVB doub 477 n y C6 O YVB doub 478 n n C10 C9 YVB doub 479 n y C8 C9 YVB sing 480 n y C9 C13 YVB sing 481 n n C13 N1 YVB doub 482 n y C13 N2 YVB sing 483 n y N1 C14 YVB sing 484 n y N2 C15 YVB sing 485 n y N3 C20 YVB sing 486 n n C14 C15 YVB doub 487 n y C14 C19 YVB sing 488 n y C15 C16 YVB sing 489 n y C20 C19 YVB sing 490 n n C20 O1 YVB doub 491 n n C19 C18 YVB doub 492 n y C16 C17 YVB doub 493 n y C18 C17 YVB sing 494 n y C8 H2 YVB sing 495 n n N2 H3 YVB sing 496 n n N3 H4 YVB sing 497 n n N3 H5 YVB sing 498 n n C4 H6 YVB sing 499 n n C3 H7 YVB sing 500 n n C3 H8 YVB sing 501 n n C3 H9 YVB sing 502 n n N4 H10 YVB sing 503 n n N4 H11 YVB sing 504 n n N H12 YVB sing 505 n n C H13 YVB sing 506 n n C H14 YVB sing 507 n n C H15 YVB sing 508 n n C10 H16 YVB sing 509 n n C11 H17 YVB sing 510 n n C12 H18 YVB sing 511 n n C16 H19 YVB sing 512 n n C17 H20 YVB sing 513 n n C18 H21 YVB sing 514 n n C22 H22 YVB sing 515 n n # _atom_sites.entry_id 8FZ1 _atom_sites.fract_transf_matrix[1][1] 0.01046 _atom_sites.fract_transf_matrix[1][2] 0.006039 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012079 _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] 0.007763 _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 E 3 CIT A 1 1401 1401 CIT CIT . F 4 DMS A 1 1402 1601 DMS DMS . G 5 YVB A 1 1403 1901 YVB XXX . H 3 CIT A 1 1404 2101 CIT CIT . I 4 DMS A 1 1405 2201 DMS DMS . J 6 EDO A 1 1406 2401 EDO PGE . K 6 EDO A 1 1407 2501 EDO PGE . L 4 DMS B 1 1601 1601 DMS DMS . M 3 CIT B 1 1602 1701 CIT CIT . N 5 YVB B 1 1603 2301 YVB XXX . O 4 DMS B 1 1604 2401 DMS DMS . P 6 EDO B 1 1605 2701 EDO PGE . Q 6 EDO B 1 1606 2801 EDO PGE . R 6 EDO B 1 1607 2901 EDO PGE . S 7 HOH A 1 1501 19 HOH HOH . S 7 HOH A 2 1502 2 HOH HOH . S 7 HOH A 3 1503 18 HOH HOH . S 7 HOH A 4 1504 3 HOH HOH . S 7 HOH A 5 1505 14 HOH HOH . S 7 HOH A 6 1506 13 HOH HOH . T 7 HOH B 1 1701 6 HOH HOH . T 7 HOH B 2 1702 12 HOH HOH . T 7 HOH B 3 1703 20 HOH HOH . T 7 HOH B 4 1704 4 HOH HOH . T 7 HOH B 5 1705 11 HOH HOH . T 7 HOH B 6 1706 7 HOH HOH . T 7 HOH B 7 1707 17 HOH HOH . T 7 HOH B 8 1708 5 HOH HOH . T 7 HOH B 9 1709 8 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 N N1 YVB . . . G 5 37.252 12.383 -8.339 1 53.9 ? N1 YVB 1403 A 1 HETATM 2 C C7 YVB . . . G 5 40.848 10.914 -10.251 1 94.19 ? C7 YVB 1403 A 1 HETATM 3 C C8 YVB . . . G 5 39.8 11.335 -9.44 1 90.43 ? C8 YVB 1403 A 1 HETATM 4 N N2 YVB . . . G 5 36.631 10.277 -7.92 1 52.84 ? N2 YVB 1403 A 1 HETATM 5 C C9 YVB . . . G 5 38.616 10.606 -9.383 1 64.52 ? C9 YVB 1403 A 1 HETATM 6 O O1 YVB . . . G 5 35.384 15.735 -6.271 1 44.89 ? O1 YVB 1403 A 1 HETATM 7 C C1 YVB . . . G 5 45.105 15.757 -10.926 1 116.47 ? C1 YVB 1403 A 1 HETATM 8 C C5 YVB . . . G 5 43.13 13.779 -11.077 1 138.87 ? C5 YVB 1403 A 1 HETATM 9 C C6 YVB . . . G 5 42.109 11.717 -10.224 1 106.01 ? C6 YVB 1403 A 1 HETATM 10 N N3 YVB . . . G 5 36.867 15.198 -7.849 1 47.17 ? N3 YVB 1403 A 1 HETATM 11 C C4 YVB . . . G 5 42.878 14.97 -10.403 1 131.96 ? C4 YVB 1403 A 1 HETATM 12 C C3 YVB . . . G 5 43.563 17.208 -9.521 1 93.56 ? C3 YVB 1403 A 1 HETATM 13 C C2 YVB . . . G 5 43.852 15.958 -10.31 1 124.12 ? C2 YVB 1403 A 1 HETATM 14 N N4 YVB . . . G 5 44.643 12.4 -12.347 1 112.83 ? N4 YVB 1403 A 1 HETATM 15 N N YVB . . . G 5 42.166 12.749 -11.098 1 116.4 ? N YVB 1403 A 1 HETATM 16 C C YVB . . . G 5 46.189 16.806 -10.855 1 94.27 ? C YVB 1403 A 1 HETATM 17 O O YVB . . . G 5 43.006 11.464 -9.421 1 117.7 ? O YVB 1403 A 1 HETATM 18 C C10 YVB . . . G 5 38.492 9.444 -10.132 1 71.86 ? C10 YVB 1403 A 1 HETATM 19 C C11 YVB . . . G 5 39.527 9.026 -10.948 1 59.35 ? C11 YVB 1403 A 1 HETATM 20 C C12 YVB . . . G 5 40.698 9.761 -11.015 1 92.53 ? C12 YVB 1403 A 1 HETATM 21 C C13 YVB . . . G 5 37.504 11.098 -8.56 1 50.58 ? C13 YVB 1403 A 1 HETATM 22 C C14 YVB . . . G 5 36.151 12.393 -7.493 1 47 ? C14 YVB 1403 A 1 HETATM 23 C C15 YVB . . . G 5 35.748 11.086 -7.232 1 45.53 ? C15 YVB 1403 A 1 HETATM 24 C C16 YVB . . . G 5 34.645 10.792 -6.445 1 46.17 ? C16 YVB 1403 A 1 HETATM 25 C C17 YVB . . . G 5 33.933 11.857 -5.918 1 44.19 ? C17 YVB 1403 A 1 HETATM 26 C C18 YVB . . . G 5 34.329 13.169 -6.155 1 42.99 ? C18 YVB 1403 A 1 HETATM 27 C C19 YVB . . . G 5 35.451 13.467 -6.926 1 44.54 ? C19 YVB 1403 A 1 HETATM 28 C C20 YVB . . . G 5 35.898 14.892 -7.007 1 43.22 ? C20 YVB 1403 A 1 HETATM 29 C C21 YVB . . . G 5 44.374 13.568 -11.691 1 137.27 ? C21 YVB 1403 A 1 HETATM 30 C C22 YVB . . . G 5 45.348 14.569 -11.609 1 130.03 ? C22 YVB 1403 A 1 # _model_server_stats.io_time_ms 135 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 260 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #