data_5VUA # _model_server_result.job_id nfqzG60BJGZ1DFf0xGY6Lw _model_server_result.datetime_utc '2025-01-12 01:02:50' _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 5vua # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5VUA # _exptl.entry_id 5VUA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.435 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2Z)-6-methoxy-7-(piperazin-1-ylmethyl)-2-(1H-pyrrolo[2,3-c]pyridin-3-ylmethylidene)-1-benzofuran-3-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 90 _cell.angle_gamma 120 _cell.entry_id 5VUA _cell.length_a 98.14 _cell.length_b 98.14 _cell.length_c 80.51 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VUA _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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,D,E _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C22 H22 N4 O3' _chem_comp.formula_weight 390.435 _chem_comp.id 8GX _chem_comp.mon_nstd_flag . _chem_comp.name (2Z)-6-methoxy-7-(piperazin-1-ylmethyl)-2-(1H-pyrrolo[2,3-c]pyridin-3-ylmethylidene)-1-benzofuran-3-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 C12 C11 8GX sing 1 n n C12 N13 8GX sing 2 n n C11 N10 8GX sing 3 n n N13 C14 8GX sing 4 n n C01 O02 8GX sing 5 n n O02 C03 8GX sing 6 n n N10 C09 8GX sing 7 n n N10 C15 8GX sing 8 n n C14 C15 8GX sing 9 n n C09 C08 8GX sing 10 n n C03 C08 8GX doub 11 n y C03 C04 8GX sing 12 n y C08 C07 8GX sing 13 n y C04 C05 8GX doub 14 n y C07 C06 8GX doub 15 n y C07 O16 8GX sing 16 n n C05 C06 8GX sing 17 n y C25 C24 8GX sing 18 n y C25 N26 8GX doub 19 n y C06 C28 8GX sing 20 n n O16 C17 8GX sing 21 n n C24 C23 8GX doub 22 n y N26 C27 8GX sing 23 n y C17 C28 8GX sing 24 n n C17 C18 8GX doub 25 z n C28 O29 8GX doub 26 n n C27 C22 8GX doub 27 n y C23 C22 8GX sing 28 n y C23 C19 8GX sing 29 n y C22 N21 8GX sing 30 n y C18 C19 8GX sing 31 n n C19 C20 8GX doub 32 n y N21 C20 8GX sing 33 n y C15 H1 8GX sing 34 n n C15 H2 8GX sing 35 n n C20 H3 8GX sing 36 n n C24 H4 8GX sing 37 n n C01 H5 8GX sing 38 n n C01 H6 8GX sing 39 n n C01 H7 8GX sing 40 n n C04 H8 8GX sing 41 n n C05 H9 8GX sing 42 n n C09 H10 8GX sing 43 n n C09 H11 8GX sing 44 n n C11 H13 8GX sing 45 n n C11 H14 8GX sing 46 n n C12 H15 8GX sing 47 n n C12 H16 8GX sing 48 n n N13 H17 8GX sing 49 n n C14 H19 8GX sing 50 n n C14 H20 8GX sing 51 n n C18 H21 8GX sing 52 n n N21 H22 8GX sing 53 n n C25 H23 8GX sing 54 n n C27 H24 8GX sing 55 n n # _atom_sites.entry_id 5VUA _atom_sites.fract_transf_matrix[1][1] 0.01019 _atom_sites.fract_transf_matrix[1][2] 0.005883 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011766 _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] 0.012421 _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 GOL B 1 401 1 GOL GOL . C 3 PO4 B 1 402 1 PO4 PO4 . D 4 8GX B 1 403 1 8GX LIG . E 5 HOH B 1 501 171 HOH HOH . E 5 HOH B 2 502 180 HOH HOH . E 5 HOH B 3 503 175 HOH HOH . E 5 HOH B 4 504 3 HOH HOH . E 5 HOH B 5 505 179 HOH HOH . E 5 HOH B 6 506 176 HOH HOH . E 5 HOH B 7 507 57 HOH HOH . E 5 HOH B 8 508 157 HOH HOH . E 5 HOH B 9 509 200 HOH HOH . E 5 HOH B 10 510 95 HOH HOH . E 5 HOH B 11 511 140 HOH HOH . E 5 HOH B 12 512 73 HOH HOH . E 5 HOH B 13 513 46 HOH HOH . E 5 HOH B 14 514 145 HOH HOH . E 5 HOH B 15 515 88 HOH HOH . E 5 HOH B 16 516 32 HOH HOH . E 5 HOH B 17 517 92 HOH HOH . E 5 HOH B 18 518 174 HOH HOH . E 5 HOH B 19 519 39 HOH HOH . E 5 HOH B 20 520 55 HOH HOH . E 5 HOH B 21 521 155 HOH HOH . E 5 HOH B 22 522 45 HOH HOH . E 5 HOH B 23 523 40 HOH HOH . E 5 HOH B 24 524 54 HOH HOH . E 5 HOH B 25 525 86 HOH HOH . E 5 HOH B 26 526 210 HOH HOH . E 5 HOH B 27 527 65 HOH HOH . E 5 HOH B 28 528 26 HOH HOH . E 5 HOH B 29 529 186 HOH HOH . E 5 HOH B 30 530 9 HOH HOH . E 5 HOH B 31 531 78 HOH HOH . E 5 HOH B 32 532 109 HOH HOH . E 5 HOH B 33 533 47 HOH HOH . E 5 HOH B 34 534 33 HOH HOH . E 5 HOH B 35 535 127 HOH HOH . E 5 HOH B 36 536 22 HOH HOH . E 5 HOH B 37 537 43 HOH HOH . E 5 HOH B 38 538 5 HOH HOH . E 5 HOH B 39 539 129 HOH HOH . E 5 HOH B 40 540 29 HOH HOH . E 5 HOH B 41 541 108 HOH HOH . E 5 HOH B 42 542 199 HOH HOH . E 5 HOH B 43 543 15 HOH HOH . E 5 HOH B 44 544 8 HOH HOH . E 5 HOH B 45 545 69 HOH HOH . E 5 HOH B 46 546 122 HOH HOH . E 5 HOH B 47 547 124 HOH HOH . E 5 HOH B 48 548 63 HOH HOH . E 5 HOH B 49 549 70 HOH HOH . E 5 HOH B 50 550 123 HOH HOH . E 5 HOH B 51 551 30 HOH HOH . E 5 HOH B 52 552 16 HOH HOH . E 5 HOH B 53 553 126 HOH HOH . E 5 HOH B 54 554 13 HOH HOH . E 5 HOH B 55 555 198 HOH HOH . E 5 HOH B 56 556 203 HOH HOH . E 5 HOH B 57 557 38 HOH HOH . E 5 HOH B 58 558 49 HOH HOH . E 5 HOH B 59 559 11 HOH HOH . E 5 HOH B 60 560 53 HOH HOH . E 5 HOH B 61 561 101 HOH HOH . E 5 HOH B 62 562 17 HOH HOH . E 5 HOH B 63 563 152 HOH HOH . E 5 HOH B 64 564 23 HOH HOH . E 5 HOH B 65 565 170 HOH HOH . E 5 HOH B 66 566 132 HOH HOH . E 5 HOH B 67 567 66 HOH HOH . E 5 HOH B 68 568 168 HOH HOH . E 5 HOH B 69 569 113 HOH HOH . E 5 HOH B 70 570 75 HOH HOH . E 5 HOH B 71 571 166 HOH HOH . E 5 HOH B 72 572 10 HOH HOH . E 5 HOH B 73 573 115 HOH HOH . E 5 HOH B 74 574 116 HOH HOH . E 5 HOH B 75 575 7 HOH HOH . E 5 HOH B 76 576 41 HOH HOH . E 5 HOH B 77 577 52 HOH HOH . E 5 HOH B 78 578 4 HOH HOH . E 5 HOH B 79 579 72 HOH HOH . E 5 HOH B 80 580 195 HOH HOH . E 5 HOH B 81 581 206 HOH HOH . E 5 HOH B 82 582 156 HOH HOH . E 5 HOH B 83 583 12 HOH HOH . E 5 HOH B 84 584 61 HOH HOH . E 5 HOH B 85 585 142 HOH HOH . E 5 HOH B 86 586 99 HOH HOH . E 5 HOH B 87 587 35 HOH HOH . E 5 HOH B 88 588 139 HOH HOH . E 5 HOH B 89 589 56 HOH HOH . E 5 HOH B 90 590 34 HOH HOH . E 5 HOH B 91 591 165 HOH HOH . E 5 HOH B 92 592 144 HOH HOH . E 5 HOH B 93 593 188 HOH HOH . E 5 HOH B 94 594 50 HOH HOH . E 5 HOH B 95 595 21 HOH HOH . E 5 HOH B 96 596 98 HOH HOH . E 5 HOH B 97 597 209 HOH HOH . E 5 HOH B 98 598 105 HOH HOH . E 5 HOH B 99 599 18 HOH HOH . E 5 HOH B 100 600 134 HOH HOH . E 5 HOH B 101 601 100 HOH HOH . E 5 HOH B 102 602 119 HOH HOH . E 5 HOH B 103 603 162 HOH HOH . E 5 HOH B 104 604 190 HOH HOH . E 5 HOH B 105 605 25 HOH HOH . E 5 HOH B 106 606 135 HOH HOH . E 5 HOH B 107 607 192 HOH HOH . E 5 HOH B 108 608 143 HOH HOH . E 5 HOH B 109 609 164 HOH HOH . E 5 HOH B 110 610 81 HOH HOH . E 5 HOH B 111 611 87 HOH HOH . E 5 HOH B 112 612 1 HOH HOH . E 5 HOH B 113 613 2 HOH HOH . E 5 HOH B 114 614 107 HOH HOH . E 5 HOH B 115 615 137 HOH HOH . E 5 HOH B 116 616 82 HOH HOH . E 5 HOH B 117 617 84 HOH HOH . E 5 HOH B 118 618 27 HOH HOH . E 5 HOH B 119 619 80 HOH HOH . E 5 HOH B 120 620 189 HOH HOH . E 5 HOH B 121 621 191 HOH HOH . E 5 HOH B 122 622 51 HOH HOH . E 5 HOH B 123 623 204 HOH HOH . E 5 HOH B 124 624 83 HOH HOH . E 5 HOH B 125 625 91 HOH HOH . E 5 HOH B 126 626 71 HOH HOH . E 5 HOH B 127 627 48 HOH HOH . E 5 HOH B 128 628 151 HOH HOH . E 5 HOH B 129 629 59 HOH HOH . E 5 HOH B 130 630 79 HOH HOH . E 5 HOH B 131 631 94 HOH HOH . E 5 HOH B 132 632 6 HOH HOH . E 5 HOH B 133 633 14 HOH HOH . E 5 HOH B 134 634 36 HOH HOH . E 5 HOH B 135 635 44 HOH HOH . E 5 HOH B 136 636 24 HOH HOH . E 5 HOH B 137 637 60 HOH HOH . E 5 HOH B 138 638 114 HOH HOH . E 5 HOH B 139 639 102 HOH HOH . E 5 HOH B 140 640 104 HOH HOH . E 5 HOH B 141 641 31 HOH HOH . E 5 HOH B 142 642 147 HOH HOH . E 5 HOH B 143 643 193 HOH HOH . E 5 HOH B 144 644 213 HOH HOH . E 5 HOH B 145 645 93 HOH HOH . E 5 HOH B 146 646 120 HOH HOH . E 5 HOH B 147 647 19 HOH HOH . E 5 HOH B 148 648 28 HOH HOH . E 5 HOH B 149 649 184 HOH HOH . E 5 HOH B 150 650 148 HOH HOH . E 5 HOH B 151 651 136 HOH HOH . E 5 HOH B 152 652 130 HOH HOH . E 5 HOH B 153 653 42 HOH HOH . E 5 HOH B 154 654 62 HOH HOH . E 5 HOH B 155 655 202 HOH HOH . E 5 HOH B 156 656 201 HOH HOH . E 5 HOH B 157 657 185 HOH HOH . E 5 HOH B 158 658 58 HOH HOH . E 5 HOH B 159 659 74 HOH HOH . E 5 HOH B 160 660 118 HOH HOH . E 5 HOH B 161 661 110 HOH HOH . E 5 HOH B 162 662 158 HOH HOH . E 5 HOH B 163 663 77 HOH HOH . E 5 HOH B 164 664 111 HOH HOH . E 5 HOH B 165 665 106 HOH HOH . E 5 HOH B 166 666 128 HOH HOH . E 5 HOH B 167 667 37 HOH HOH . E 5 HOH B 168 668 133 HOH HOH . E 5 HOH B 169 669 64 HOH HOH . E 5 HOH B 170 670 150 HOH HOH . E 5 HOH B 171 671 207 HOH HOH . E 5 HOH B 172 672 20 HOH HOH . E 5 HOH B 173 673 89 HOH HOH . E 5 HOH B 174 674 67 HOH HOH . E 5 HOH B 175 675 194 HOH HOH . E 5 HOH B 176 676 76 HOH HOH . E 5 HOH B 177 677 172 HOH HOH . E 5 HOH B 178 678 173 HOH HOH . E 5 HOH B 179 679 68 HOH HOH . E 5 HOH B 180 680 90 HOH HOH . E 5 HOH B 181 681 187 HOH HOH . E 5 HOH B 182 682 138 HOH HOH . E 5 HOH B 183 683 131 HOH HOH . E 5 HOH B 184 684 159 HOH HOH . E 5 HOH B 185 685 177 HOH HOH . E 5 HOH B 186 686 97 HOH HOH . E 5 HOH B 187 687 167 HOH HOH . E 5 HOH B 188 688 121 HOH HOH . E 5 HOH B 189 689 183 HOH HOH . E 5 HOH B 190 690 96 HOH HOH . E 5 HOH B 191 691 182 HOH HOH . E 5 HOH B 192 692 181 HOH HOH . E 5 HOH B 193 693 146 HOH HOH . E 5 HOH B 194 694 103 HOH HOH . E 5 HOH B 195 695 169 HOH HOH . E 5 HOH B 196 696 141 HOH HOH . E 5 HOH B 197 697 117 HOH HOH . E 5 HOH B 198 698 197 HOH HOH . E 5 HOH B 199 699 163 HOH HOH . E 5 HOH B 200 700 149 HOH HOH . E 5 HOH B 201 701 161 HOH HOH . E 5 HOH B 202 702 208 HOH HOH . E 5 HOH B 203 703 212 HOH HOH . E 5 HOH B 204 704 196 HOH HOH . E 5 HOH B 205 705 85 HOH HOH . E 5 HOH B 206 706 205 HOH HOH . E 5 HOH B 207 707 160 HOH HOH . E 5 HOH B 208 708 153 HOH HOH . E 5 HOH B 209 709 211 HOH HOH . E 5 HOH B 210 710 178 HOH HOH . E 5 HOH B 211 711 112 HOH HOH . E 5 HOH B 212 712 154 HOH HOH . E 5 HOH B 213 713 125 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 C15 8GX . . . D 4 17.386 -37.259 -4.347 1 30.33 ? C15 8GX 403 B 1 HETATM 2 C C17 8GX . . . D 4 17.541 -35.591 -0.137 1 29.7 ? C17 8GX 403 B 1 HETATM 3 C C20 8GX . . . D 4 19.214 -38.051 2.207 1 27.03 ? C20 8GX 403 B 1 HETATM 4 C C22 8GX . . . D 4 20.466 -39.067 0.629 1 28.86 ? C22 8GX 403 B 1 HETATM 5 C C24 8GX . . . D 4 19.819 -37.97 -1.414 1 28.92 ? C24 8GX 403 B 1 HETATM 6 C C28 8GX . . . D 4 16.517 -34.488 -0.134 1 27.53 ? C28 8GX 403 B 1 HETATM 7 C C01 8GX . . . D 4 16.43 -32.173 -6.238 1 33.89 ? C01 8GX 403 B 1 HETATM 8 O O02 8GX . . . D 4 17.259 -33.094 -5.53 1 40.97 ? O02 8GX 403 B 1 HETATM 9 C C03 8GX . . . D 4 17.009 -33.382 -4.182 1 33.12 ? C03 8GX 403 B 1 HETATM 10 C C04 8GX . . . D 4 16.057 -32.652 -3.456 1 36.98 ? C04 8GX 403 B 1 HETATM 11 C C05 8GX . . . D 4 15.827 -32.941 -2.11 1 37.07 ? C05 8GX 403 B 1 HETATM 12 C C06 8GX . . . D 4 16.543 -33.96 -1.511 1 31.09 ? C06 8GX 403 B 1 HETATM 13 C C07 8GX . . . D 4 17.507 -34.704 -2.245 1 25.13 ? C07 8GX 403 B 1 HETATM 14 C C08 8GX . . . D 4 17.773 -34.45 -3.606 1 35.76 ? C08 8GX 403 B 1 HETATM 15 C C09 8GX . . . D 4 18.797 -35.191 -4.468 1 32.89 ? C09 8GX 403 B 1 HETATM 16 N N10 8GX . . . D 4 18.209 -36.409 -5.222 1 37.11 ? N10 8GX 403 B 1 HETATM 17 C C11 8GX . . . D 4 17.38 -36.063 -6.433 1 40.71 ? C11 8GX 403 B 1 HETATM 18 C C12 8GX . . . D 4 17.001 -37.353 -7.218 1 37.22 ? C12 8GX 403 B 1 HETATM 19 N N13 8GX . . . D 4 16.194 -38.287 -6.314 1 31.23 1 N13 8GX 403 B 1 HETATM 20 C C14 8GX . . . D 4 16.999 -38.578 -5.059 1 27.75 ? C14 8GX 403 B 1 HETATM 21 O O16 8GX . . . D 4 18.091 -35.664 -1.44 1 30.21 ? O16 8GX 403 B 1 HETATM 22 C C18 8GX . . . D 4 17.873 -36.359 0.908 1 30.41 ? C18 8GX 403 B 1 HETATM 23 C C19 8GX . . . D 4 18.864 -37.434 1.015 1 31.64 ? C19 8GX 403 B 1 HETATM 24 N N21 8GX . . . D 4 20.175 -39.031 1.995 1 30.16 ? N21 8GX 403 B 1 HETATM 25 C C23 8GX . . . D 4 19.657 -38.068 -0.019 1 25.85 ? C23 8GX 403 B 1 HETATM 26 C C25 8GX . . . D 4 20.723 -38.812 -2.029 1 28.54 ? C25 8GX 403 B 1 HETATM 27 N N26 8GX . . . D 4 21.492 -39.764 -1.396 1 32.85 ? N26 8GX 403 B 1 HETATM 28 C C27 8GX . . . D 4 21.362 -39.889 -0.073 1 32.73 ? C27 8GX 403 B 1 HETATM 29 O O29 8GX . . . D 4 15.83 -34.12 0.805 1 31.66 ? O29 8GX 403 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 51 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 363 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #