data_8J3B # _model_server_result.job_id Hhokz2ShvXlhXFM2EW0xDQ _model_server_result.datetime_utc '2025-07-13 04:06:50' _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 8j3b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 8J3B # _exptl.entry_id 8J3B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 474.55 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-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 108.336 _cell.angle_gamma 90 _cell.entry_id 8J3B _cell.length_a 55.385 _cell.length_b 98.943 _cell.length_c 59.388 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8J3B _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 C N N ? 2 D N N # 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 covale ? covale1 A SG CYS 143 A CYS 145 1_555 C C34 V2M . A V2M 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? covale ? covale2 B SG CYS 143 B CYS 145 1_555 D C34 V2M . B V2M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? # _chem_comp.formula 'C24 H34 N4 O6' _chem_comp.formula_weight 474.55 _chem_comp.id V2M _chem_comp.mon_nstd_flag . _chem_comp.name N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'N-[(2S)-1-({(2S)-4-hydroxy-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, bound form' # 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 O37 C36 V2M sing 358 n n C36 C34 V2M sing 359 n n O35 C34 V2M sing 360 n n C20 C18 V2M sing 361 n n C34 C24 V2M sing 362 n n O22 C21 V2M doub 363 n n C17 C18 V2M sing 364 n n C17 C15 V2M sing 365 n n C18 C19 V2M sing 366 n n C24 N23 V2M sing 367 n n C24 C26 V2M sing 368 n n C21 N23 V2M sing 369 n n C21 C15 V2M sing 370 n n C1 O2 V2M sing 371 n n C15 N14 V2M sing 372 n n C29 C30 V2M sing 373 n n C29 C27 V2M sing 374 n n O2 C3 V2M sing 375 n n N14 C12 V2M sing 376 n n C26 C27 V2M sing 377 n n C10 C11 V2M sing 378 n y C10 C9 V2M doub 379 n y C30 N31 V2M sing 380 n n C27 C32 V2M sing 381 n n C3 C11 V2M doub 382 n y C3 C4 V2M sing 383 n y C12 C9 V2M sing 384 n n C12 O13 V2M doub 385 n n C11 C7 V2M sing 386 n y C9 N8 V2M sing 387 n y C4 C5 V2M doub 388 n y N31 C32 V2M sing 389 n n C32 O33 V2M doub 390 n n C7 N8 V2M sing 391 n y C7 C6 V2M doub 392 n y C5 C6 V2M sing 393 n y C1 H1 V2M sing 394 n n C1 H2 V2M sing 395 n n C1 H3 V2M sing 396 n n C4 H4 V2M sing 397 n n C5 H5 V2M sing 398 n n C6 H6 V2M sing 399 n n N8 H7 V2M sing 400 n n C10 H8 V2M sing 401 n n N14 H9 V2M sing 402 n n C15 H10 V2M sing 403 n n C17 H11 V2M sing 404 n n C17 H12 V2M sing 405 n n C18 H13 V2M sing 406 n n C19 H14 V2M sing 407 n n C19 H15 V2M sing 408 n n C19 H16 V2M sing 409 n n C20 H17 V2M sing 410 n n C20 H18 V2M sing 411 n n C20 H19 V2M sing 412 n n N23 H20 V2M sing 413 n n C24 H21 V2M sing 414 n n C26 H22 V2M sing 415 n n C26 H23 V2M sing 416 n n C27 H24 V2M sing 417 n n C29 H25 V2M sing 418 n n C29 H26 V2M sing 419 n n C30 H27 V2M sing 420 n n C30 H28 V2M sing 421 n n N31 H29 V2M sing 422 n n C34 H30 V2M sing 423 n n O35 H31 V2M sing 424 n n C36 H32 V2M sing 425 n n C36 H33 V2M sing 426 n n O37 H34 V2M sing 427 n n # _atom_sites.entry_id 8J3B _atom_sites.fract_transf_matrix[1][1] 0.018055 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005984 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010107 _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] 0.017739 _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 V2M A 1 501 401 V2M V2M . D 2 V2M B 1 401 401 V2M V2M . E 3 HOH A 1 601 59 HOH HOH . E 3 HOH A 2 602 79 HOH HOH . E 3 HOH A 3 603 67 HOH HOH . E 3 HOH A 4 604 76 HOH HOH . E 3 HOH A 5 605 82 HOH HOH . E 3 HOH A 6 606 62 HOH HOH . E 3 HOH A 7 607 130 HOH HOH . E 3 HOH A 8 608 7 HOH HOH . E 3 HOH A 9 609 36 HOH HOH . E 3 HOH A 10 610 17 HOH HOH . E 3 HOH A 11 611 141 HOH HOH . E 3 HOH A 12 612 13 HOH HOH . E 3 HOH A 13 613 93 HOH HOH . E 3 HOH A 14 614 44 HOH HOH . E 3 HOH A 15 615 23 HOH HOH . E 3 HOH A 16 616 20 HOH HOH . E 3 HOH A 17 617 85 HOH HOH . E 3 HOH A 18 618 54 HOH HOH . E 3 HOH A 19 619 138 HOH HOH . E 3 HOH A 20 620 107 HOH HOH . E 3 HOH A 21 621 110 HOH HOH . E 3 HOH A 22 622 83 HOH HOH . E 3 HOH A 23 623 28 HOH HOH . E 3 HOH A 24 624 112 HOH HOH . E 3 HOH A 25 625 10 HOH HOH . E 3 HOH A 26 626 87 HOH HOH . E 3 HOH A 27 627 39 HOH HOH . E 3 HOH A 28 628 123 HOH HOH . E 3 HOH A 29 629 12 HOH HOH . E 3 HOH A 30 630 115 HOH HOH . E 3 HOH A 31 631 106 HOH HOH . E 3 HOH A 32 632 108 HOH HOH . E 3 HOH A 33 633 68 HOH HOH . E 3 HOH A 34 634 1 HOH HOH . E 3 HOH A 35 635 73 HOH HOH . E 3 HOH A 36 636 50 HOH HOH . E 3 HOH A 37 637 40 HOH HOH . E 3 HOH A 38 638 99 HOH HOH . E 3 HOH A 39 639 136 HOH HOH . E 3 HOH A 40 640 122 HOH HOH . E 3 HOH A 41 641 27 HOH HOH . E 3 HOH A 42 642 57 HOH HOH . E 3 HOH A 43 643 134 HOH HOH . E 3 HOH A 44 644 38 HOH HOH . E 3 HOH A 45 645 49 HOH HOH . E 3 HOH A 46 646 4 HOH HOH . E 3 HOH A 47 647 48 HOH HOH . E 3 HOH A 48 648 78 HOH HOH . E 3 HOH A 49 649 96 HOH HOH . E 3 HOH A 50 650 111 HOH HOH . E 3 HOH A 51 651 92 HOH HOH . E 3 HOH A 52 652 60 HOH HOH . E 3 HOH A 53 653 117 HOH HOH . E 3 HOH A 54 654 71 HOH HOH . E 3 HOH A 55 655 103 HOH HOH . E 3 HOH A 56 656 94 HOH HOH . E 3 HOH A 57 657 53 HOH HOH . E 3 HOH A 58 658 46 HOH HOH . E 3 HOH A 59 659 26 HOH HOH . E 3 HOH A 60 660 88 HOH HOH . E 3 HOH A 61 661 124 HOH HOH . E 3 HOH A 62 662 8 HOH HOH . E 3 HOH A 63 663 47 HOH HOH . E 3 HOH A 64 664 104 HOH HOH . E 3 HOH A 65 665 63 HOH HOH . E 3 HOH A 66 666 118 HOH HOH . E 3 HOH A 67 667 84 HOH HOH . E 3 HOH A 68 668 135 HOH HOH . E 3 HOH A 69 669 125 HOH HOH . E 3 HOH A 70 670 142 HOH HOH . F 3 HOH B 1 501 133 HOH HOH . F 3 HOH B 2 502 55 HOH HOH . F 3 HOH B 3 503 43 HOH HOH . F 3 HOH B 4 504 90 HOH HOH . F 3 HOH B 5 505 56 HOH HOH . F 3 HOH B 6 506 22 HOH HOH . F 3 HOH B 7 507 64 HOH HOH . F 3 HOH B 8 508 72 HOH HOH . F 3 HOH B 9 509 15 HOH HOH . F 3 HOH B 10 510 102 HOH HOH . F 3 HOH B 11 511 2 HOH HOH . F 3 HOH B 12 512 98 HOH HOH . F 3 HOH B 13 513 101 HOH HOH . F 3 HOH B 14 514 11 HOH HOH . F 3 HOH B 15 515 14 HOH HOH . F 3 HOH B 16 516 128 HOH HOH . F 3 HOH B 17 517 5 HOH HOH . F 3 HOH B 18 518 100 HOH HOH . F 3 HOH B 19 519 95 HOH HOH . F 3 HOH B 20 520 58 HOH HOH . F 3 HOH B 21 521 129 HOH HOH . F 3 HOH B 22 522 137 HOH HOH . F 3 HOH B 23 523 51 HOH HOH . F 3 HOH B 24 524 33 HOH HOH . F 3 HOH B 25 525 97 HOH HOH . F 3 HOH B 26 526 81 HOH HOH . F 3 HOH B 27 527 126 HOH HOH . F 3 HOH B 28 528 21 HOH HOH . F 3 HOH B 29 529 9 HOH HOH . F 3 HOH B 30 530 30 HOH HOH . F 3 HOH B 31 531 74 HOH HOH . F 3 HOH B 32 532 3 HOH HOH . F 3 HOH B 33 533 120 HOH HOH . F 3 HOH B 34 534 61 HOH HOH . F 3 HOH B 35 535 109 HOH HOH . F 3 HOH B 36 536 32 HOH HOH . F 3 HOH B 37 537 34 HOH HOH . F 3 HOH B 38 538 35 HOH HOH . F 3 HOH B 39 539 16 HOH HOH . F 3 HOH B 40 540 70 HOH HOH . F 3 HOH B 41 541 19 HOH HOH . F 3 HOH B 42 542 121 HOH HOH . F 3 HOH B 43 543 41 HOH HOH . F 3 HOH B 44 544 65 HOH HOH . F 3 HOH B 45 545 105 HOH HOH . F 3 HOH B 46 546 66 HOH HOH . F 3 HOH B 47 547 37 HOH HOH . F 3 HOH B 48 548 69 HOH HOH . F 3 HOH B 49 549 6 HOH HOH . F 3 HOH B 50 550 116 HOH HOH . F 3 HOH B 51 551 25 HOH HOH . F 3 HOH B 52 552 77 HOH HOH . F 3 HOH B 53 553 119 HOH HOH . F 3 HOH B 54 554 42 HOH HOH . F 3 HOH B 55 555 45 HOH HOH . F 3 HOH B 56 556 24 HOH HOH . F 3 HOH B 57 557 18 HOH HOH . F 3 HOH B 58 558 29 HOH HOH . F 3 HOH B 59 559 132 HOH HOH . F 3 HOH B 60 560 86 HOH HOH . F 3 HOH B 61 561 89 HOH HOH . F 3 HOH B 62 562 140 HOH HOH . F 3 HOH B 63 563 113 HOH HOH . F 3 HOH B 64 564 52 HOH HOH . F 3 HOH B 65 565 91 HOH HOH . F 3 HOH B 66 566 131 HOH HOH . F 3 HOH B 67 567 75 HOH HOH . F 3 HOH B 68 568 114 HOH HOH . F 3 HOH B 69 569 80 HOH HOH . F 3 HOH B 70 570 127 HOH HOH . F 3 HOH B 71 571 139 HOH HOH . F 3 HOH B 72 572 31 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 C1 V2M . . . D 2 13.283 24.739 27.394 1 34.68 ? C1 V2M 401 B 1 HETATM 2 O O2 V2M . . . D 2 13.02 23.4 27 1 32.55 ? O2 V2M 401 B 1 HETATM 3 C C3 V2M . . . D 2 12.136 23.192 25.984 1 34.2 ? C3 V2M 401 B 1 HETATM 4 C C4 V2M . . . D 2 11.62 24.187 25.189 1 29.99 ? C4 V2M 401 B 1 HETATM 5 C C5 V2M . . . D 2 10.715 23.883 24.167 1 33.02 ? C5 V2M 401 B 1 HETATM 6 C C6 V2M . . . D 2 10.305 22.605 23.912 1 32.38 ? C6 V2M 401 B 1 HETATM 7 C C7 V2M . . . D 2 10.824 21.597 24.717 1 32.25 ? C7 V2M 401 B 1 HETATM 8 N N8 V2M . . . D 2 10.599 20.252 24.705 1 30.64 ? N8 V2M 401 B 1 HETATM 9 C C9 V2M . . . D 2 11.342 19.666 25.702 1 29.17 ? C9 V2M 401 B 1 HETATM 10 C C10 V2M . . . D 2 12.052 20.629 26.367 1 29.43 ? C10 V2M 401 B 1 HETATM 11 C C11 V2M . . . D 2 11.738 21.871 25.756 1 30.74 ? C11 V2M 401 B 1 HETATM 12 C C12 V2M . . . D 2 11.247 18.214 25.879 1 29.61 ? C12 V2M 401 B 1 HETATM 13 O O13 V2M . . . D 2 10.504 17.534 25.177 1 29.52 ? O13 V2M 401 B 1 HETATM 14 N N14 V2M . . . D 2 12.003 17.695 26.848 1 28.63 ? N14 V2M 401 B 1 HETATM 15 C C15 V2M . . . D 2 11.949 16.278 27.156 1 26.13 ? C15 V2M 401 B 1 HETATM 16 C C17 V2M . . . D 2 13.044 15.967 28.173 1 26.21 ? C17 V2M 401 B 1 HETATM 17 C C18 V2M . . . D 2 14.47 16.116 27.647 1 28 ? C18 V2M 401 B 1 HETATM 18 C C19 V2M . . . D 2 15.479 16.08 28.785 1 26.41 ? C19 V2M 401 B 1 HETATM 19 C C20 V2M . . . D 2 14.786 15.042 26.622 1 27.31 ? C20 V2M 401 B 1 HETATM 20 C C21 V2M . . . D 2 10.582 15.869 27.71 1 30.34 ? C21 V2M 401 B 1 HETATM 21 O O22 V2M . . . D 2 10.013 16.573 28.536 1 29.44 ? O22 V2M 401 B 1 HETATM 22 N N23 V2M . . . D 2 10.089 14.697 27.303 1 25.16 ? N23 V2M 401 B 1 HETATM 23 C C24 V2M . . . D 2 8.822 14.218 27.825 1 28.82 ? C24 V2M 401 B 1 HETATM 24 C C26 V2M . . . D 2 7.824 13.864 26.719 1 27.26 ? C26 V2M 401 B 1 HETATM 25 C C27 V2M . . . D 2 7.266 15.17 26.143 1 31.06 ? C27 V2M 401 B 1 HETATM 26 C C29 V2M . . . D 2 6.524 16.032 27.16 1 27.41 ? C29 V2M 401 B 1 HETATM 27 C C30 V2M . . . D 2 5.404 16.696 26.376 1 29.1 ? C30 V2M 401 B 1 HETATM 28 N N31 V2M . . . D 2 5.259 15.843 25.204 1 30.6 ? N31 V2M 401 B 1 HETATM 29 C C32 V2M . . . D 2 6.271 15.015 25.008 1 29.31 ? C32 V2M 401 B 1 HETATM 30 O O33 V2M . . . D 2 6.415 14.291 24.029 1 24.96 ? O33 V2M 401 B 1 HETATM 31 C C34 V2M . . . D 2 9.145 12.952 28.615 1 30.97 ? C34 V2M 401 B 1 HETATM 32 O O35 V2M . . . D 2 8.151 12.27 29.034 1 27.48 ? O35 V2M 401 B 1 HETATM 33 C C36 V2M . . . D 2 10.244 13.171 29.681 1 28.41 ? C36 V2M 401 B 1 HETATM 34 O O37 V2M . . . D 2 10.358 12.173 30.662 1 28.81 ? O37 V2M 401 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 224 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 34 #