data_3VSO # _model_server_result.job_id GgMrkzEzlgxlDDS0rOnjxA _model_server_result.datetime_utc '2024-12-26 15:03:49' _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 3vso # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 3VSO # _exptl.entry_id 3VSO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 509.596 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2-benzyl-3-[4-propoxy-3-({[4-(pyrimidin-2-yl)benzoyl]amino}methyl)phenyl]propanoic acid' _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 102.79 _cell.angle_gamma 90 _cell.entry_id 3VSO _cell.length_a 93.346 _cell.length_b 61.706 _cell.length_c 118.984 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VSO _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1 A,C,D 2 1 B,E 2 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 -46.673 30.853 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 'C31 H31 N3 O4' _chem_comp.formula_weight 509.596 _chem_comp.id EK1 _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2-benzyl-3-[4-propoxy-3-({[4-(pyrimidin-2-yl)benzoyl]amino}methyl)phenyl]propanoic acid' _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 C84 C85 EK1 doub 83 n y C84 N83 EK1 sing 84 n y C85 C86 EK1 sing 85 n y N83 C82 EK1 doub 86 n y C86 N81 EK1 doub 87 n y C82 N81 EK1 sing 88 n y C82 C98 EK1 sing 89 n n C98 C99 EK1 doub 90 n y C98 C19 EK1 sing 91 n y C99 C22 EK1 sing 92 n y C19 C17 EK1 doub 93 n y C22 C87 EK1 doub 94 n y C13 C14 EK1 sing 95 n n C13 C12 EK1 sing 96 n n C17 C87 EK1 sing 97 n y C87 C97 EK1 sing 98 n n O99 C97 EK1 doub 99 n n C97 N99 EK1 sing 100 n n C12 O3 EK1 sing 101 n n O3 C9 EK1 sing 102 n n N99 C15 EK1 sing 103 n n C15 C8 EK1 sing 104 n n C9 C8 EK1 doub 105 n y C9 C10 EK1 sing 106 n y C8 C7 EK1 sing 107 n y C10 C11 EK1 doub 108 n y C7 C6 EK1 doub 109 n y C11 C6 EK1 sing 110 n y C6 C5 EK1 sing 111 n n C5 C2 EK1 sing 112 n n C3 C2 EK1 sing 113 n n C3 C4 EK1 sing 114 n n C55 C54 EK1 doub 115 n y C55 C4 EK1 sing 116 n y C2 C1 EK1 sing 117 n n C54 C53 EK1 sing 118 n y C4 C51 EK1 doub 119 n y C1 O1 EK1 doub 120 n n C1 O2 EK1 sing 121 n n C53 C52 EK1 doub 122 n y C51 C52 EK1 sing 123 n y C84 H1 EK1 sing 124 n n C85 H2 EK1 sing 125 n n C86 H3 EK1 sing 126 n n C99 H4 EK1 sing 127 n n C19 H5 EK1 sing 128 n n C17 H6 EK1 sing 129 n n C22 H7 EK1 sing 130 n n C15 H8 EK1 sing 131 n n C12 H9 EK1 sing 132 n n C13 H10 EK1 sing 133 n n C14 H11 EK1 sing 134 n n C14 H12 EK1 sing 135 n n C14 H13 EK1 sing 136 n n C10 H14 EK1 sing 137 n n C11 H15 EK1 sing 138 n n C5 H16 EK1 sing 139 n n C5 H17 EK1 sing 140 n n C2 H18 EK1 sing 141 n n C3 H19 EK1 sing 142 n n C3 H20 EK1 sing 143 n n C51 H21 EK1 sing 144 n n C52 H22 EK1 sing 145 n n C53 H23 EK1 sing 146 n n C54 H24 EK1 sing 147 n n C55 H25 EK1 sing 148 n n C7 H26 EK1 sing 149 n n O2 H27 EK1 sing 150 n n N99 H28 EK1 sing 151 n n C15 H29 EK1 sing 152 n n C12 H30 EK1 sing 153 n n C13 H31 EK1 sing 154 n n # _atom_sites.entry_id 3VSO _atom_sites.fract_transf_matrix[1][1] 0.010713 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002432 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016206 _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] 0.008618 _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 EK1 A 1 501 1 EK1 EK1 . D 3 HOH A 1 601 13 HOH HOH . D 3 HOH A 2 602 14 HOH HOH . D 3 HOH A 3 603 15 HOH HOH . D 3 HOH A 4 604 16 HOH HOH . D 3 HOH A 5 605 17 HOH HOH . D 3 HOH A 6 606 18 HOH HOH . D 3 HOH A 7 607 19 HOH HOH . D 3 HOH A 8 608 20 HOH HOH . D 3 HOH A 9 609 21 HOH HOH . D 3 HOH A 10 610 22 HOH HOH . D 3 HOH A 11 611 23 HOH HOH . D 3 HOH A 12 612 24 HOH HOH . D 3 HOH A 13 613 25 HOH HOH . D 3 HOH A 14 614 26 HOH HOH . D 3 HOH A 15 615 29 HOH HOH . D 3 HOH A 16 616 30 HOH HOH . D 3 HOH A 17 617 36 HOH HOH . D 3 HOH A 18 618 38 HOH HOH . D 3 HOH A 19 619 39 HOH HOH . D 3 HOH A 20 620 40 HOH HOH . D 3 HOH A 21 621 44 HOH HOH . D 3 HOH A 22 622 50 HOH HOH . D 3 HOH A 23 623 52 HOH HOH . D 3 HOH A 24 624 53 HOH HOH . D 3 HOH A 25 625 57 HOH HOH . D 3 HOH A 26 626 58 HOH HOH . D 3 HOH A 27 627 59 HOH HOH . D 3 HOH A 28 628 60 HOH HOH . D 3 HOH A 29 629 66 HOH HOH . D 3 HOH A 30 630 71 HOH HOH . D 3 HOH A 31 631 72 HOH HOH . D 3 HOH A 32 632 73 HOH HOH . D 3 HOH A 33 633 74 HOH HOH . D 3 HOH A 34 634 75 HOH HOH . D 3 HOH A 35 635 76 HOH HOH . D 3 HOH A 36 636 77 HOH HOH . D 3 HOH A 37 637 78 HOH HOH . D 3 HOH A 38 638 79 HOH HOH . D 3 HOH A 39 639 80 HOH HOH . D 3 HOH A 40 640 81 HOH HOH . D 3 HOH A 41 641 82 HOH HOH . D 3 HOH A 42 642 84 HOH HOH . D 3 HOH A 43 643 87 HOH HOH . D 3 HOH A 44 644 88 HOH HOH . D 3 HOH A 45 645 89 HOH HOH . D 3 HOH A 46 646 90 HOH HOH . D 3 HOH A 47 647 91 HOH HOH . D 3 HOH A 48 648 92 HOH HOH . D 3 HOH A 49 649 93 HOH HOH . D 3 HOH A 50 650 111 HOH HOH . D 3 HOH A 51 651 112 HOH HOH . D 3 HOH A 52 652 113 HOH HOH . D 3 HOH A 53 653 114 HOH HOH . E 3 HOH B 1 501 1 HOH HOH . E 3 HOH B 2 502 2 HOH HOH . E 3 HOH B 3 503 3 HOH HOH . E 3 HOH B 4 504 4 HOH HOH . E 3 HOH B 5 505 5 HOH HOH . E 3 HOH B 6 506 6 HOH HOH . E 3 HOH B 7 507 7 HOH HOH . E 3 HOH B 8 508 8 HOH HOH . E 3 HOH B 9 509 9 HOH HOH . E 3 HOH B 10 510 10 HOH HOH . E 3 HOH B 11 511 11 HOH HOH . E 3 HOH B 12 512 12 HOH HOH . E 3 HOH B 13 513 27 HOH HOH . E 3 HOH B 14 514 28 HOH HOH . E 3 HOH B 15 515 31 HOH HOH . E 3 HOH B 16 516 32 HOH HOH . E 3 HOH B 17 517 33 HOH HOH . E 3 HOH B 18 518 34 HOH HOH . E 3 HOH B 19 519 35 HOH HOH . E 3 HOH B 20 520 37 HOH HOH . E 3 HOH B 21 521 41 HOH HOH . E 3 HOH B 22 522 42 HOH HOH . E 3 HOH B 23 523 43 HOH HOH . E 3 HOH B 24 524 45 HOH HOH . E 3 HOH B 25 525 46 HOH HOH . E 3 HOH B 26 526 47 HOH HOH . E 3 HOH B 27 527 48 HOH HOH . E 3 HOH B 28 528 49 HOH HOH . E 3 HOH B 29 529 51 HOH HOH . E 3 HOH B 30 530 54 HOH HOH . E 3 HOH B 31 531 55 HOH HOH . E 3 HOH B 32 532 56 HOH HOH . E 3 HOH B 33 533 61 HOH HOH . E 3 HOH B 34 534 62 HOH HOH . E 3 HOH B 35 535 63 HOH HOH . E 3 HOH B 36 536 64 HOH HOH . E 3 HOH B 37 537 65 HOH HOH . E 3 HOH B 38 538 67 HOH HOH . E 3 HOH B 39 539 68 HOH HOH . E 3 HOH B 40 540 69 HOH HOH . E 3 HOH B 41 541 70 HOH HOH . E 3 HOH B 42 542 83 HOH HOH . E 3 HOH B 43 543 85 HOH HOH . E 3 HOH B 44 544 86 HOH HOH . E 3 HOH B 45 545 94 HOH HOH . E 3 HOH B 46 546 95 HOH HOH . E 3 HOH B 47 547 96 HOH HOH . E 3 HOH B 48 548 97 HOH HOH . E 3 HOH B 49 549 98 HOH HOH . E 3 HOH B 50 550 99 HOH HOH . E 3 HOH B 51 551 100 HOH HOH . E 3 HOH B 52 552 101 HOH HOH . E 3 HOH B 53 553 102 HOH HOH . E 3 HOH B 54 554 103 HOH HOH . E 3 HOH B 55 555 104 HOH HOH . E 3 HOH B 56 556 105 HOH HOH . E 3 HOH B 57 557 106 HOH HOH . E 3 HOH B 58 558 107 HOH HOH . E 3 HOH B 59 559 108 HOH HOH . E 3 HOH B 60 560 109 HOH HOH . E 3 HOH B 61 561 110 HOH HOH . E 3 HOH B 62 562 115 HOH HOH . E 3 HOH B 63 563 116 HOH HOH . E 3 HOH B 64 564 117 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 N81 EK1 . . . C 2 16.619 75.693 8.073 1 63.77 ? N81 EK1 501 A 1 HETATM 2 C C82 EK1 . . . C 2 17.129 74.471 7.898 1 60.29 ? C82 EK1 501 A 1 HETATM 3 N N83 EK1 . . . C 2 18.152 74.231 7.06 1 54.89 ? N83 EK1 501 A 1 HETATM 4 C C84 EK1 . . . C 2 18.714 75.234 6.382 1 58.67 ? C84 EK1 501 A 1 HETATM 5 C C85 EK1 . . . C 2 18.227 76.524 6.537 1 62.58 ? C85 EK1 501 A 1 HETATM 6 C C86 EK1 . . . C 2 17.153 76.727 7.413 1 66.2 ? C86 EK1 501 A 1 HETATM 7 C C99 EK1 . . . C 2 17.28 72.142 8.626 1 51.54 ? C99 EK1 501 A 1 HETATM 8 C C98 EK1 . . . C 2 16.55 73.327 8.584 1 57.82 ? C98 EK1 501 A 1 HETATM 9 C C19 EK1 . . . C 2 15.282 73.395 9.144 1 57.3 ? C19 EK1 501 A 1 HETATM 10 C C17 EK1 . . . C 2 14.741 72.274 9.773 1 55.85 ? C17 EK1 501 A 1 HETATM 11 C C87 EK1 . . . C 2 15.479 71.095 9.817 1 49.32 ? C87 EK1 501 A 1 HETATM 12 C C22 EK1 . . . C 2 16.738 71.041 9.246 1 52.52 ? C22 EK1 501 A 1 HETATM 13 C C97 EK1 . . . C 2 14.941 69.878 10.473 1 54.49 ? C97 EK1 501 A 1 HETATM 14 O O99 EK1 . . . C 2 13.897 69.419 10.072 1 55.86 ? O99 EK1 501 A 1 HETATM 15 N N99 EK1 . . . C 2 15.76 69.282 11.613 1 60.5 ? N99 EK1 501 A 1 HETATM 16 C C15 EK1 . . . C 2 15.45 68.104 12.427 1 57.65 ? C15 EK1 501 A 1 HETATM 17 C C8 EK1 . . . C 2 16.578 67.574 13.298 1 54.52 ? C8 EK1 501 A 1 HETATM 18 C C9 EK1 . . . C 2 17.732 67.164 12.652 1 56.21 ? C9 EK1 501 A 1 HETATM 19 O O3 EK1 . . . C 2 17.776 67.254 11.245 1 57.6 ? O3 EK1 501 A 1 HETATM 20 C C12 EK1 . . . C 2 18.923 66.932 10.575 1 53.29 ? C12 EK1 501 A 1 HETATM 21 C C13 EK1 . . . C 2 19.443 67.952 9.592 1 54.29 ? C13 EK1 501 A 1 HETATM 22 C C14 EK1 . . . C 2 18.842 69.27 9.622 1 50.54 ? C14 EK1 501 A 1 HETATM 23 C C10 EK1 . . . C 2 18.807 66.673 13.384 1 54.44 ? C10 EK1 501 A 1 HETATM 24 C C11 EK1 . . . C 2 18.736 66.593 14.773 1 59.5 ? C11 EK1 501 A 1 HETATM 25 C C6 EK1 . . . C 2 17.58 67.01 15.442 1 53.6 ? C6 EK1 501 A 1 HETATM 26 C C5 EK1 . . . C 2 17.532 66.907 16.992 1 58.67 ? C5 EK1 501 A 1 HETATM 27 C C2 EK1 . . . C 2 18.687 67.529 17.818 1 55.98 ? C2 EK1 501 A 1 HETATM 28 C C3 EK1 . . . C 2 18.728 69.008 17.478 1 58.18 ? C3 EK1 501 A 1 HETATM 29 C C4 EK1 . . . C 2 19.781 69.919 18.231 1 61.1 ? C4 EK1 501 A 1 HETATM 30 C C51 EK1 . . . C 2 19.838 69.933 19.618 1 53.7 ? C51 EK1 501 A 1 HETATM 31 C C52 EK1 . . . C 2 20.754 70.721 20.284 1 59.54 ? C52 EK1 501 A 1 HETATM 32 C C53 EK1 . . . C 2 21.626 71.51 19.548 1 62.75 ? C53 EK1 501 A 1 HETATM 33 C C54 EK1 . . . C 2 21.568 71.493 18.161 1 61.58 ? C54 EK1 501 A 1 HETATM 34 C C55 EK1 . . . C 2 20.653 70.699 17.488 1 60.53 ? C55 EK1 501 A 1 HETATM 35 C C7 EK1 . . . C 2 16.504 67.499 14.703 1 56.08 ? C7 EK1 501 A 1 HETATM 36 C C1 EK1 . . . C 2 18.579 67.439 19.286 1 56.92 ? C1 EK1 501 A 1 HETATM 37 O O1 EK1 . . . C 2 19.302 66.635 19.936 1 58.72 ? O1 EK1 501 A 1 HETATM 38 O O2 EK1 . . . C 2 17.78 68.204 19.946 1 49.77 ? O2 EK1 501 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #