data_5RCC # _model_server_result.job_id CJIOTQqbE_V46F-LEut86Q _model_server_result.datetime_utc '2024-11-17 00:28:52' _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 5rcc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5RCC # _exptl.entry_id 5RCC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 210.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-cyclopentyl-1-(piperazin-1-yl)propan-1-one _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 109.21 _cell.angle_gamma 90 _cell.entry_id 5RCC _cell.length_a 45.172 _cell.length_b 72.854 _cell.length_c 52.521 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5RCC _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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,D,E,F,G,H,I _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 344 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 255 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 379 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 290 _struct_conn.ptnr2_symmetry 1_555 _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 2.068 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C12 H22 N2 O' _chem_comp.formula_weight 210.316 _chem_comp.id RDV _chem_comp.mon_nstd_flag . _chem_comp.name 3-cyclopentyl-1-(piperazin-1-yl)propan-1-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 C9 RDV sing 305 n n N1 C10 RDV sing 306 n n C9 C8 RDV sing 307 n n C8 N RDV sing 308 n n C11 C10 RDV sing 309 n n C11 N RDV sing 310 n n N C7 RDV sing 311 n n C7 O RDV doub 312 n n C7 C6 RDV sing 313 n n C6 C5 RDV sing 314 n n C5 C3 RDV sing 315 n n C4 C3 RDV sing 316 n n C4 C RDV sing 317 n n C3 C2 RDV sing 318 n n C C1 RDV sing 319 n n C2 C1 RDV sing 320 n n C4 H1 RDV sing 321 n n C4 H2 RDV sing 322 n n C5 H3 RDV sing 323 n n C5 H4 RDV sing 324 n n C6 H5 RDV sing 325 n n C6 H6 RDV sing 326 n n N1 H7 RDV sing 327 n n C8 H9 RDV sing 328 n n C8 H10 RDV sing 329 n n C9 H11 RDV sing 330 n n C9 H12 RDV sing 331 n n C10 H13 RDV sing 332 n n C10 H14 RDV sing 333 n n C11 H15 RDV sing 334 n n C11 H16 RDV sing 335 n n C3 H17 RDV sing 336 n n C2 H18 RDV sing 337 n n C2 H19 RDV sing 338 n n C1 H20 RDV sing 339 n n C1 H21 RDV sing 340 n n C H22 RDV sing 341 n n C H23 RDV sing 342 n n # _atom_sites.entry_id 5RCC _atom_sites.fract_transf_matrix[1][1] 0.022138 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007712 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013726 _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] 0.020162 _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 RDV A 1 401 401 RDV XXX . C 2 RDV A 1 402 501 RDV XXX . D 3 DMS A 1 403 601 DMS DMS . E 4 GOL A 1 404 701 GOL GOL . F 4 GOL A 1 405 401 GOL GOL . G 4 GOL A 1 406 403 GOL GOL . H 5 ACT A 1 407 405 ACT ACT . I 6 HOH A 1 501 230 HOH HOH . I 6 HOH A 2 502 63 HOH HOH . I 6 HOH A 3 503 224 HOH HOH . I 6 HOH A 4 504 48 HOH HOH . I 6 HOH A 5 505 236 HOH HOH . I 6 HOH A 6 506 64 HOH HOH . I 6 HOH A 7 507 136 HOH HOH . I 6 HOH A 8 508 249 HOH HOH . I 6 HOH A 9 509 241 HOH HOH . I 6 HOH A 10 510 207 HOH HOH . I 6 HOH A 11 511 211 HOH HOH . I 6 HOH A 12 512 155 HOH HOH . I 6 HOH A 13 513 140 HOH HOH . I 6 HOH A 14 514 197 HOH HOH . I 6 HOH A 15 515 52 HOH HOH . I 6 HOH A 16 516 242 HOH HOH . I 6 HOH A 17 517 126 HOH HOH . I 6 HOH A 18 518 133 HOH HOH . I 6 HOH A 19 519 214 HOH HOH . I 6 HOH A 20 520 10 HOH HOH . I 6 HOH A 21 521 186 HOH HOH . I 6 HOH A 22 522 156 HOH HOH . I 6 HOH A 23 523 55 HOH HOH . I 6 HOH A 24 524 183 HOH HOH . I 6 HOH A 25 525 127 HOH HOH . I 6 HOH A 26 526 165 HOH HOH . I 6 HOH A 27 527 13 HOH HOH . I 6 HOH A 28 528 24 HOH HOH . I 6 HOH A 29 529 185 HOH HOH . I 6 HOH A 30 530 132 HOH HOH . I 6 HOH A 31 531 19 HOH HOH . I 6 HOH A 32 532 31 HOH HOH . I 6 HOH A 33 533 82 HOH HOH . I 6 HOH A 34 534 43 HOH HOH . I 6 HOH A 35 535 21 HOH HOH . I 6 HOH A 36 536 18 HOH HOH . I 6 HOH A 37 537 95 HOH HOH . I 6 HOH A 38 538 170 HOH HOH . I 6 HOH A 39 539 157 HOH HOH . I 6 HOH A 40 540 57 HOH HOH . I 6 HOH A 41 541 65 HOH HOH . I 6 HOH A 42 542 158 HOH HOH . I 6 HOH A 43 543 98 HOH HOH . I 6 HOH A 44 544 66 HOH HOH . I 6 HOH A 45 545 27 HOH HOH . I 6 HOH A 46 546 41 HOH HOH . I 6 HOH A 47 547 3 HOH HOH . I 6 HOH A 48 548 212 HOH HOH . I 6 HOH A 49 549 248 HOH HOH . I 6 HOH A 50 550 47 HOH HOH . I 6 HOH A 51 551 159 HOH HOH . I 6 HOH A 52 552 171 HOH HOH . I 6 HOH A 53 553 100 HOH HOH . I 6 HOH A 54 554 120 HOH HOH . I 6 HOH A 55 555 85 HOH HOH . I 6 HOH A 56 556 192 HOH HOH . I 6 HOH A 57 557 46 HOH HOH . I 6 HOH A 58 558 2 HOH HOH . I 6 HOH A 59 559 23 HOH HOH . I 6 HOH A 60 560 38 HOH HOH . I 6 HOH A 61 561 35 HOH HOH . I 6 HOH A 62 562 33 HOH HOH . I 6 HOH A 63 563 7 HOH HOH . I 6 HOH A 64 564 154 HOH HOH . I 6 HOH A 65 565 14 HOH HOH . I 6 HOH A 66 566 50 HOH HOH . I 6 HOH A 67 567 220 HOH HOH . I 6 HOH A 68 568 162 HOH HOH . I 6 HOH A 69 569 124 HOH HOH . I 6 HOH A 70 570 22 HOH HOH . I 6 HOH A 71 571 206 HOH HOH . I 6 HOH A 72 572 169 HOH HOH . I 6 HOH A 73 573 119 HOH HOH . I 6 HOH A 74 574 25 HOH HOH . I 6 HOH A 75 575 44 HOH HOH . I 6 HOH A 76 576 60 HOH HOH . I 6 HOH A 77 577 37 HOH HOH . I 6 HOH A 78 578 20 HOH HOH . I 6 HOH A 79 579 30 HOH HOH . I 6 HOH A 80 580 17 HOH HOH . I 6 HOH A 81 581 59 HOH HOH . I 6 HOH A 82 582 209 HOH HOH . I 6 HOH A 83 583 141 HOH HOH . I 6 HOH A 84 584 8 HOH HOH . I 6 HOH A 85 585 117 HOH HOH . I 6 HOH A 86 586 176 HOH HOH . I 6 HOH A 87 587 174 HOH HOH . I 6 HOH A 88 588 12 HOH HOH . I 6 HOH A 89 589 112 HOH HOH . I 6 HOH A 90 590 114 HOH HOH . I 6 HOH A 91 591 103 HOH HOH . I 6 HOH A 92 592 123 HOH HOH . I 6 HOH A 93 593 187 HOH HOH . I 6 HOH A 94 594 26 HOH HOH . I 6 HOH A 95 595 61 HOH HOH . I 6 HOH A 96 596 226 HOH HOH . I 6 HOH A 97 597 142 HOH HOH . I 6 HOH A 98 598 116 HOH HOH . I 6 HOH A 99 599 246 HOH HOH . I 6 HOH A 100 600 42 HOH HOH . I 6 HOH A 101 601 80 HOH HOH . I 6 HOH A 102 602 89 HOH HOH . I 6 HOH A 103 603 167 HOH HOH . I 6 HOH A 104 604 62 HOH HOH . I 6 HOH A 105 605 196 HOH HOH . I 6 HOH A 106 606 16 HOH HOH . I 6 HOH A 107 607 190 HOH HOH . I 6 HOH A 108 608 102 HOH HOH . I 6 HOH A 109 609 128 HOH HOH . I 6 HOH A 110 610 110 HOH HOH . I 6 HOH A 111 611 131 HOH HOH . I 6 HOH A 112 612 11 HOH HOH . I 6 HOH A 113 613 184 HOH HOH . I 6 HOH A 114 614 118 HOH HOH . I 6 HOH A 115 615 239 HOH HOH . I 6 HOH A 116 616 233 HOH HOH . I 6 HOH A 117 617 67 HOH HOH . I 6 HOH A 118 618 87 HOH HOH . I 6 HOH A 119 619 72 HOH HOH . I 6 HOH A 120 620 161 HOH HOH . I 6 HOH A 121 621 218 HOH HOH . I 6 HOH A 122 622 225 HOH HOH . I 6 HOH A 123 623 223 HOH HOH . I 6 HOH A 124 624 222 HOH HOH . I 6 HOH A 125 625 227 HOH HOH . I 6 HOH A 126 626 188 HOH HOH . I 6 HOH A 127 627 245 HOH HOH . I 6 HOH A 128 628 39 HOH HOH . I 6 HOH A 129 629 175 HOH HOH . I 6 HOH A 130 630 74 HOH HOH . I 6 HOH A 131 631 138 HOH HOH . I 6 HOH A 132 632 139 HOH HOH . I 6 HOH A 133 633 104 HOH HOH . I 6 HOH A 134 634 208 HOH HOH . I 6 HOH A 135 635 15 HOH HOH . I 6 HOH A 136 636 91 HOH HOH . I 6 HOH A 137 637 29 HOH HOH . I 6 HOH A 138 638 97 HOH HOH . I 6 HOH A 139 639 86 HOH HOH . I 6 HOH A 140 640 149 HOH HOH . I 6 HOH A 141 641 34 HOH HOH . I 6 HOH A 142 642 129 HOH HOH . I 6 HOH A 143 643 94 HOH HOH . I 6 HOH A 144 644 96 HOH HOH . I 6 HOH A 145 645 68 HOH HOH . I 6 HOH A 146 646 168 HOH HOH . I 6 HOH A 147 647 238 HOH HOH . I 6 HOH A 148 648 173 HOH HOH . I 6 HOH A 149 649 49 HOH HOH . I 6 HOH A 150 650 109 HOH HOH . I 6 HOH A 151 651 6 HOH HOH . I 6 HOH A 152 652 53 HOH HOH . I 6 HOH A 153 653 73 HOH HOH . I 6 HOH A 154 654 83 HOH HOH . I 6 HOH A 155 655 84 HOH HOH . I 6 HOH A 156 656 134 HOH HOH . I 6 HOH A 157 657 148 HOH HOH . I 6 HOH A 158 658 203 HOH HOH . I 6 HOH A 159 659 177 HOH HOH . I 6 HOH A 160 660 9 HOH HOH . I 6 HOH A 161 661 28 HOH HOH . I 6 HOH A 162 662 56 HOH HOH . I 6 HOH A 163 663 151 HOH HOH . I 6 HOH A 164 664 219 HOH HOH . I 6 HOH A 165 665 88 HOH HOH . I 6 HOH A 166 666 163 HOH HOH . I 6 HOH A 167 667 152 HOH HOH . I 6 HOH A 168 668 75 HOH HOH . I 6 HOH A 169 669 81 HOH HOH . I 6 HOH A 170 670 251 HOH HOH . I 6 HOH A 171 671 179 HOH HOH . I 6 HOH A 172 672 144 HOH HOH . I 6 HOH A 173 673 216 HOH HOH . I 6 HOH A 174 674 221 HOH HOH . I 6 HOH A 175 675 204 HOH HOH . I 6 HOH A 176 676 122 HOH HOH . I 6 HOH A 177 677 135 HOH HOH . I 6 HOH A 178 678 58 HOH HOH . I 6 HOH A 179 679 232 HOH HOH . I 6 HOH A 180 680 235 HOH HOH . I 6 HOH A 181 681 250 HOH HOH . I 6 HOH A 182 682 146 HOH HOH . I 6 HOH A 183 683 125 HOH HOH . I 6 HOH A 184 684 121 HOH HOH . I 6 HOH A 185 685 54 HOH HOH . I 6 HOH A 186 686 69 HOH HOH . I 6 HOH A 187 687 107 HOH HOH . I 6 HOH A 188 688 166 HOH HOH . I 6 HOH A 189 689 115 HOH HOH . I 6 HOH A 190 690 189 HOH HOH . I 6 HOH A 191 691 130 HOH HOH . I 6 HOH A 192 692 113 HOH HOH . I 6 HOH A 193 693 92 HOH HOH . I 6 HOH A 194 694 71 HOH HOH . I 6 HOH A 195 695 191 HOH HOH . I 6 HOH A 196 696 145 HOH HOH . I 6 HOH A 197 697 106 HOH HOH . I 6 HOH A 198 698 153 HOH HOH . I 6 HOH A 199 699 147 HOH HOH . I 6 HOH A 200 700 180 HOH HOH . I 6 HOH A 201 701 200 HOH HOH . I 6 HOH A 202 702 164 HOH HOH . I 6 HOH A 203 703 202 HOH HOH . I 6 HOH A 204 704 193 HOH HOH . I 6 HOH A 205 705 172 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 C4 RDV . C . B 2 32.163 8.429 63.664 0.27 13.14 ? C4 RDV 401 A 1 HETATM 2 C C4 RDV . D . B 2 26.089 3.468 60.725 0.26 16.58 ? C4 RDV 401 A 1 HETATM 3 C C5 RDV . C . B 2 29.922 7.717 62.86 0.27 13.38 ? C5 RDV 401 A 1 HETATM 4 C C5 RDV . D . B 2 28.286 2.704 59.653 0.26 15.34 ? C5 RDV 401 A 1 HETATM 5 C C6 RDV . C . B 2 30.223 8.336 61.502 0.27 13.08 ? C6 RDV 401 A 1 HETATM 6 C C6 RDV . D . B 2 27.894 3.788 58.642 0.26 15.72 ? C6 RDV 401 A 1 HETATM 7 N N1 RDV . C . B 2 29.422 4.763 58.318 0.27 12.19 1 N1 RDV 401 A 1 HETATM 8 N N1 RDV . D . B 2 27.903 8.37 60.796 0.26 17.12 1 N1 RDV 401 A 1 HETATM 9 C C7 RDV . C . B 2 29.098 8.076 60.526 0.27 12.6 ? C7 RDV 401 A 1 HETATM 10 C C7 RDV . D . B 2 28.902 4.906 58.732 0.26 15.82 ? C7 RDV 401 A 1 HETATM 11 C C8 RDV . C . B 2 28.379 6.982 58.403 0.27 12.69 ? C8 RDV 401 A 1 HETATM 12 C C8 RDV . D . B 2 29.462 7.142 59.349 0.26 15.53 ? C8 RDV 401 A 1 HETATM 13 C C9 RDV . C . B 2 28.127 5.496 58.332 0.27 11.85 ? C9 RDV 401 A 1 HETATM 14 C C9 RDV . D . B 2 29.28 7.831 60.68 0.26 16.47 ? C9 RDV 401 A 1 HETATM 15 C C10 RDV . C . B 2 30.318 5.203 59.437 0.27 11.75 ? C10 RDV 401 A 1 HETATM 16 C C10 RDV . D . B 2 26.889 7.318 60.534 0.26 16.62 ? C10 RDV 401 A 1 HETATM 17 C C11 RDV . C . B 2 30.66 6.658 59.27 0.27 12.22 ? C11 RDV 401 A 1 HETATM 18 C C11 RDV . D . B 2 27.088 6.722 59.164 0.26 16.7 ? C11 RDV 401 A 1 HETATM 19 O O RDV . C . B 2 28.001 8.538 60.734 0.27 14.76 ? O RDV 401 A 1 HETATM 20 O O RDV . D . B 2 30.13 4.652 58.664 0.26 14.3 ? O RDV 401 A 1 HETATM 21 C C3 RDV . C . B 2 30.672 8.328 64 0.27 13.62 ? C3 RDV 401 A 1 HETATM 22 C C3 RDV . D . B 2 27.143 2.342 60.606 0.26 15.33 ? C3 RDV 401 A 1 HETATM 23 C C2 RDV . C . B 2 30.708 7.396 65.19 0.27 14.2 ? C2 RDV 401 A 1 HETATM 24 C C2 RDV . D . B 2 26.243 1.221 60.131 0.26 15.32 ? C2 RDV 401 A 1 HETATM 25 C C1 RDV . C . B 2 31.818 7.946 66.01 0.27 13.8 ? C1 RDV 401 A 1 HETATM 26 C C1 RDV . D . B 2 25.016 1.334 61.015 0.26 16.06 ? C1 RDV 401 A 1 HETATM 27 C C RDV . C . B 2 32.884 8.281 64.998 0.27 13.99 ? C RDV 401 A 1 HETATM 28 C C RDV . D . B 2 24.765 2.779 61.118 0.26 17.09 ? C RDV 401 A 1 HETATM 29 N N RDV . C . B 2 29.345 7.267 59.477 0.27 12.25 ? N RDV 401 A 1 HETATM 30 N N RDV . D . B 2 28.431 6.157 59.016 0.26 16.06 ? N RDV 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 30 #