data_5U5L # _model_server_result.job_id tvFlnL2gjMDzTHtpYnZYPw _model_server_result.datetime_utc '2024-11-25 08:37:33' _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 5u5l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5U5L # _exptl.entry_id 5U5L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 397.448 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5S)-5-({4-[(6-methoxy-1-methyl-1H-benzimidazol-2-yl)methoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione _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 102.22 _cell.angle_gamma 90 _cell.entry_id 5U5L _cell.length_a 93.394 _cell.length_b 62.097 _cell.length_c 118.47 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U5L _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D 1 1 B,E 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_455 x-1/2,y+1/2,z 1 0 0 0 1 0 0 0 1 -46.697 31.0485 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C20 H19 N3 O4 S' _chem_comp.formula_weight 397.448 _chem_comp.id 7VA _chem_comp.mon_nstd_flag . _chem_comp.name (5S)-5-({4-[(6-methoxy-1-methyl-1H-benzimidazol-2-yl)methoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione _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 O27 C28 7VA sing 1 n n O27 C23 7VA sing 2 n n C23 C22 7VA doub 3 n y C23 C24 7VA sing 4 n y C22 C19 7VA sing 5 n y C24 C25 7VA doub 6 n y C26 N18 7VA sing 7 n n C19 N18 7VA sing 8 n y C19 C20 7VA doub 9 n y N18 C17 7VA sing 10 n y C25 C20 7VA sing 11 n y C20 N21 7VA sing 12 n y C17 N21 7VA doub 13 n y C17 C16 7VA sing 14 n n C16 O15 7VA sing 15 n n O15 C12 7VA sing 16 n n C12 C11 7VA doub 17 n y C12 C13 7VA sing 18 n y C11 C10 7VA sing 19 n y C13 C14 7VA doub 20 n y C10 C09 7VA doub 21 n y C14 C09 7VA sing 22 n y C09 C08 7VA sing 23 n n S04 C03 7VA sing 24 n n S04 C05 7VA sing 25 n n C08 C03 7VA sing 26 n n C03 C02 7VA sing 27 n n O06 C05 7VA doub 28 n n C05 N01 7VA sing 29 n n C02 N01 7VA sing 30 n n C02 O07 7VA doub 31 n n C10 H1 7VA sing 32 n n C13 H2 7VA sing 33 n n C22 H3 7VA sing 34 n n C24 H4 7VA sing 35 n n C26 H5 7VA sing 36 n n C26 H6 7VA sing 37 n n C26 H7 7VA sing 38 n n C28 H8 7VA sing 39 n n C28 H9 7VA sing 40 n n C28 H10 7VA sing 41 n n N01 H11 7VA sing 42 n n C08 H12 7VA sing 43 n n C08 H13 7VA sing 44 n n C11 H14 7VA sing 45 n n C14 H15 7VA sing 46 n n C16 H16 7VA sing 47 n n C16 H17 7VA sing 48 n n C25 H18 7VA sing 49 n n C03 H19 7VA sing 50 n n # _atom_sites.entry_id 5U5L _atom_sites.fract_transf_matrix[1][1] 0.010707 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002319 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016104 _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] 0.008637 _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 C 2 7VA A 1 501 1 7VA LIG . D 3 HOH A 1 601 2 HOH HOH . D 3 HOH A 2 602 111 HOH HOH . D 3 HOH A 3 603 75 HOH HOH . D 3 HOH A 4 604 121 HOH HOH . D 3 HOH A 5 605 88 HOH HOH . D 3 HOH A 6 606 4 HOH HOH . D 3 HOH A 7 607 29 HOH HOH . D 3 HOH A 8 608 103 HOH HOH . D 3 HOH A 9 609 25 HOH HOH . D 3 HOH A 10 610 112 HOH HOH . D 3 HOH A 11 611 18 HOH HOH . D 3 HOH A 12 612 67 HOH HOH . D 3 HOH A 13 613 15 HOH HOH . D 3 HOH A 14 614 45 HOH HOH . D 3 HOH A 15 615 105 HOH HOH . D 3 HOH A 16 616 64 HOH HOH . D 3 HOH A 17 617 38 HOH HOH . D 3 HOH A 18 618 33 HOH HOH . D 3 HOH A 19 619 47 HOH HOH . D 3 HOH A 20 620 85 HOH HOH . D 3 HOH A 21 621 102 HOH HOH . D 3 HOH A 22 622 5 HOH HOH . D 3 HOH A 23 623 54 HOH HOH . D 3 HOH A 24 624 70 HOH HOH . D 3 HOH A 25 625 12 HOH HOH . D 3 HOH A 26 626 86 HOH HOH . D 3 HOH A 27 627 48 HOH HOH . D 3 HOH A 28 628 117 HOH HOH . D 3 HOH A 29 629 81 HOH HOH . D 3 HOH A 30 630 42 HOH HOH . D 3 HOH A 31 631 22 HOH HOH . D 3 HOH A 32 632 11 HOH HOH . D 3 HOH A 33 633 23 HOH HOH . D 3 HOH A 34 634 68 HOH HOH . D 3 HOH A 35 635 30 HOH HOH . D 3 HOH A 36 636 14 HOH HOH . D 3 HOH A 37 637 21 HOH HOH . D 3 HOH A 38 638 28 HOH HOH . D 3 HOH A 39 639 76 HOH HOH . D 3 HOH A 40 640 108 HOH HOH . D 3 HOH A 41 641 36 HOH HOH . D 3 HOH A 42 642 89 HOH HOH . D 3 HOH A 43 643 109 HOH HOH . D 3 HOH A 44 644 110 HOH HOH . D 3 HOH A 45 645 40 HOH HOH . D 3 HOH A 46 646 49 HOH HOH . D 3 HOH A 47 647 77 HOH HOH . D 3 HOH A 48 648 13 HOH HOH . D 3 HOH A 49 649 80 HOH HOH . D 3 HOH A 50 650 79 HOH HOH . D 3 HOH A 51 651 52 HOH HOH . D 3 HOH A 52 652 17 HOH HOH . D 3 HOH A 53 653 78 HOH HOH . D 3 HOH A 54 654 101 HOH HOH . D 3 HOH A 55 655 107 HOH HOH . D 3 HOH A 56 656 104 HOH HOH . D 3 HOH A 57 657 113 HOH HOH . D 3 HOH A 58 658 83 HOH HOH . D 3 HOH A 59 659 87 HOH HOH . E 3 HOH B 1 501 100 HOH HOH . E 3 HOH B 2 502 65 HOH HOH . E 3 HOH B 3 503 8 HOH HOH . E 3 HOH B 4 504 98 HOH HOH . E 3 HOH B 5 505 58 HOH HOH . E 3 HOH B 6 506 7 HOH HOH . E 3 HOH B 7 507 19 HOH HOH . E 3 HOH B 8 508 119 HOH HOH . E 3 HOH B 9 509 57 HOH HOH . E 3 HOH B 10 510 9 HOH HOH . E 3 HOH B 11 511 74 HOH HOH . E 3 HOH B 12 512 94 HOH HOH . E 3 HOH B 13 513 62 HOH HOH . E 3 HOH B 14 514 44 HOH HOH . E 3 HOH B 15 515 6 HOH HOH . E 3 HOH B 16 516 10 HOH HOH . E 3 HOH B 17 517 71 HOH HOH . E 3 HOH B 18 518 16 HOH HOH . E 3 HOH B 19 519 27 HOH HOH . E 3 HOH B 20 520 59 HOH HOH . E 3 HOH B 21 521 99 HOH HOH . E 3 HOH B 22 522 61 HOH HOH . E 3 HOH B 23 523 26 HOH HOH . E 3 HOH B 24 524 37 HOH HOH . E 3 HOH B 25 525 55 HOH HOH . E 3 HOH B 26 526 91 HOH HOH . E 3 HOH B 27 527 31 HOH HOH . E 3 HOH B 28 528 66 HOH HOH . E 3 HOH B 29 529 120 HOH HOH . E 3 HOH B 30 530 51 HOH HOH . E 3 HOH B 31 531 69 HOH HOH . E 3 HOH B 32 532 24 HOH HOH . E 3 HOH B 33 533 34 HOH HOH . E 3 HOH B 34 534 43 HOH HOH . E 3 HOH B 35 535 35 HOH HOH . E 3 HOH B 36 536 90 HOH HOH . E 3 HOH B 37 537 53 HOH HOH . E 3 HOH B 38 538 106 HOH HOH . E 3 HOH B 39 539 114 HOH HOH . E 3 HOH B 40 540 84 HOH HOH . E 3 HOH B 41 541 73 HOH HOH . E 3 HOH B 42 542 115 HOH HOH . E 3 HOH B 43 543 32 HOH HOH . E 3 HOH B 44 544 41 HOH HOH . E 3 HOH B 45 545 97 HOH HOH . E 3 HOH B 46 546 93 HOH HOH . E 3 HOH B 47 547 96 HOH HOH . E 3 HOH B 48 548 116 HOH HOH . E 3 HOH B 49 549 118 HOH HOH . E 3 HOH B 50 550 63 HOH HOH . E 3 HOH B 51 551 92 HOH HOH . E 3 HOH B 52 552 82 HOH HOH . E 3 HOH B 53 553 50 HOH HOH . E 3 HOH B 54 554 95 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 C10 7VA . . . C 2 -6.135 28.631 130.227 1 81.03 ? C10 7VA 501 A 1 HETATM 2 C C13 7VA . . . C 2 -8.82 29.246 129.932 1 81.07 ? C13 7VA 501 A 1 HETATM 3 C C17 7VA . . . C 2 -7.85 30.609 125.852 1 65.62 ? C17 7VA 501 A 1 HETATM 4 C C20 7VA . . . C 2 -8.604 32.589 125.347 1 61.5 ? C20 7VA 501 A 1 HETATM 5 C C22 7VA . . . C 2 -6.825 33.491 123.979 1 65.23 ? C22 7VA 501 A 1 HETATM 6 C C24 7VA . . . C 2 -8.789 34.834 124.416 1 62.64 ? C24 7VA 501 A 1 HETATM 7 C C26 7VA . . . C 2 -5.67 30.602 124.685 1 69.89 ? C26 7VA 501 A 1 HETATM 8 C C28 7VA . . . C 2 -6.949 36.949 123.707 1 71.62 ? C28 7VA 501 A 1 HETATM 9 N N01 7VA . . . C 2 -5.334 31.875 134.698 1 96.35 ? N01 7VA 501 A 1 HETATM 10 C C02 7VA . . . C 2 -6.028 30.651 134.587 1 88.37 ? C02 7VA 501 A 1 HETATM 11 C C03 7VA . . . C 2 -5.769 30.052 133.279 1 94.75 ? C03 7VA 501 A 1 HETATM 12 S S04 7VA . . . C 2 -4.735 31.108 132.483 1 99.74 ? S04 7VA 501 A 1 HETATM 13 C C05 7VA . . . C 2 -4.612 32.235 133.652 1 101.98 ? C05 7VA 501 A 1 HETATM 14 O O06 7VA . . . C 2 -3.971 33.227 133.577 1 108.41 ? O06 7VA 501 A 1 HETATM 15 O O07 7VA . . . C 2 -6.717 30.184 135.429 1 73.97 ? O07 7VA 501 A 1 HETATM 16 C C08 7VA . . . C 2 -6.319 28.723 132.755 1 90.09 ? C08 7VA 501 A 1 HETATM 17 C C09 7VA . . . C 2 -6.922 28.843 131.351 1 84.25 ? C09 7VA 501 A 1 HETATM 18 C C11 7VA . . . C 2 -6.69 28.732 128.957 1 81.12 ? C11 7VA 501 A 1 HETATM 19 C C12 7VA . . . C 2 -8.036 29.041 128.808 1 80.76 ? C12 7VA 501 A 1 HETATM 20 C C14 7VA . . . C 2 -8.266 29.145 131.199 1 81.81 ? C14 7VA 501 A 1 HETATM 21 O O15 7VA . . . C 2 -8.625 29.146 127.536 1 77.77 ? O15 7VA 501 A 1 HETATM 22 C C16 7VA . . . C 2 -7.745 29.204 126.447 1 70.65 ? C16 7VA 501 A 1 HETATM 23 N N18 7VA . . . C 2 -6.933 31.191 125.093 1 67.83 ? N18 7VA 501 A 1 HETATM 24 C C19 7VA . . . C 2 -7.375 32.437 124.758 1 65.59 ? C19 7VA 501 A 1 HETATM 25 N N21 7VA . . . C 2 -8.873 31.434 126.021 1 64.58 ? N21 7VA 501 A 1 HETATM 26 C C23 7VA . . . C 2 -7.535 34.678 123.815 1 65.02 ? C23 7VA 501 A 1 HETATM 27 C C25 7VA . . . C 2 -9.329 33.802 125.18 1 57.14 ? C25 7VA 501 A 1 HETATM 28 O O27 7VA . . . C 2 -6.989 35.715 123.046 1 66.98 ? O27 7VA 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #