data_5OOT # _model_server_result.job_id deM_4vTg6e9wcT_SCbGoNg _model_server_result.datetime_utc '2024-11-13 11:17:16' _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 5oot # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5OOT # _exptl.entry_id 5OOT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 570.685 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-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 101.99 _cell.angle_gamma 90 _cell.entry_id 5OOT _cell.length_a 45.27 _cell.length_b 66.28 _cell.length_c 54.92 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OOT _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C31 H38 N8 O3' _chem_comp.formula_weight 570.685 _chem_comp.id 4K4 _chem_comp.mon_nstd_flag . _chem_comp.name 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-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 CAO CAQ 4K4 sing 1 n n CAO CBK 4K4 sing 2 n n CAQ NBM 4K4 sing 3 n n CAT CAV 4K4 sing 4 n n CAT NBL 4K4 sing 5 n n CAV NBN 4K4 sing 6 n n OAE CBA 4K4 doub 7 n n CAB NBL 4K4 sing 8 n n NBL CAS 4K4 sing 9 n n NBN CBK 4K4 sing 10 n n NBN CAU 4K4 sing 11 n n CBK CAP 4K4 sing 12 n n NBM CBA 4K4 sing 13 n n NBM CAR 4K4 sing 14 n n CBA CBB 4K4 sing 15 n n CAP CAR 4K4 sing 16 n n CAS CAU 4K4 sing 17 n n CBB CAN 4K4 doub 18 n y CBB CAI 4K4 sing 19 n y CAN CBE 4K4 sing 20 n y CAI CAJ 4K4 doub 21 n y CAA OAZ 4K4 sing 22 n n CBE OAZ 4K4 sing 23 n n CBE CBC 4K4 doub 24 n y CAJ CBC 4K4 sing 25 n y CBC NAY 4K4 sing 26 n n NAY C2 4K4 sing 27 n n C2 N3 4K4 doub 28 n y C2 N1 4K4 sing 29 n y N3 C4 4K4 sing 30 n y CAL CAH 4K4 doub 31 n y CAL CBH 4K4 sing 32 n y N1 C6 4K4 doub 33 n y CAD NBP 4K4 sing 34 n n CAH CAG 4K4 sing 35 n y C4 NBP 4K4 sing 36 n n C4 C5 4K4 doub 37 n y NBP CBH 4K4 sing 38 n n CBH CBG 4K4 doub 39 n y C6 C5 4K4 sing 40 n y CAG CAK 4K4 doub 41 n y C5 NBO 4K4 sing 42 n n CBG CAK 4K4 sing 43 n y CBG CBF 4K4 sing 44 n n NBO CBF 4K4 sing 45 n n NBO CAC 4K4 sing 46 n n CBF OAF 4K4 doub 47 n n C6 H1 4K4 sing 48 n n CAU H2 4K4 sing 49 n n CAU H3 4K4 sing 50 n n CAS H4 4K4 sing 51 n n CAS H5 4K4 sing 52 n n CAB H7 4K4 sing 53 n n CAB H8 4K4 sing 54 n n CAB H9 4K4 sing 55 n n CAT H10 4K4 sing 56 n n CAT H11 4K4 sing 57 n n CAV H12 4K4 sing 58 n n CAV H13 4K4 sing 59 n n CBK H15 4K4 sing 60 n n CAP H16 4K4 sing 61 n n CAP H17 4K4 sing 62 n n CAR H18 4K4 sing 63 n n CAR H19 4K4 sing 64 n n CAO H20 4K4 sing 65 n n CAO H21 4K4 sing 66 n n CAQ H22 4K4 sing 67 n n CAQ H23 4K4 sing 68 n n CAN H24 4K4 sing 69 n n CAA H25 4K4 sing 70 n n CAA H26 4K4 sing 71 n n CAA H27 4K4 sing 72 n n CAI H28 4K4 sing 73 n n CAJ H29 4K4 sing 74 n n NAY H30 4K4 sing 75 n n CAD H31 4K4 sing 76 n n CAD H32 4K4 sing 77 n n CAD H33 4K4 sing 78 n n CAL H34 4K4 sing 79 n n CAH H35 4K4 sing 80 n n CAG H36 4K4 sing 81 n n CAK H37 4K4 sing 82 n n CAC H38 4K4 sing 83 n n CAC H39 4K4 sing 84 n n CAC H40 4K4 sing 85 n n # _atom_sites.entry_id 5OOT _atom_sites.fract_transf_matrix[1][1] 0.02209 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004691 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015088 _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] 0.018614 _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 4K4 A 1 301 1271 4K4 UNL . C 3 HOH A 1 401 2068 HOH HOH . C 3 HOH A 2 402 2022 HOH HOH . C 3 HOH A 3 403 2003 HOH HOH . C 3 HOH A 4 404 2049 HOH HOH . C 3 HOH A 5 405 2073 HOH HOH . C 3 HOH A 6 406 2005 HOH HOH . C 3 HOH A 7 407 2100 HOH HOH . C 3 HOH A 8 408 2052 HOH HOH . C 3 HOH A 9 409 2076 HOH HOH . C 3 HOH A 10 410 2024 HOH HOH . C 3 HOH A 11 411 2086 HOH HOH . C 3 HOH A 12 412 2078 HOH HOH . C 3 HOH A 13 413 2066 HOH HOH . C 3 HOH A 14 414 2077 HOH HOH . C 3 HOH A 15 415 2043 HOH HOH . C 3 HOH A 16 416 2110 HOH HOH . C 3 HOH A 17 417 2001 HOH HOH . C 3 HOH A 18 418 2054 HOH HOH . C 3 HOH A 19 419 2065 HOH HOH . C 3 HOH A 20 420 2123 HOH HOH . C 3 HOH A 21 421 2069 HOH HOH . C 3 HOH A 22 422 2080 HOH HOH . C 3 HOH A 23 423 2067 HOH HOH . C 3 HOH A 24 424 2106 HOH HOH . C 3 HOH A 25 425 2059 HOH HOH . C 3 HOH A 26 426 2028 HOH HOH . C 3 HOH A 27 427 2113 HOH HOH . C 3 HOH A 28 428 2033 HOH HOH . C 3 HOH A 29 429 2009 HOH HOH . C 3 HOH A 30 430 2012 HOH HOH . C 3 HOH A 31 431 2093 HOH HOH . C 3 HOH A 32 432 2117 HOH HOH . C 3 HOH A 33 433 2037 HOH HOH . C 3 HOH A 34 434 2090 HOH HOH . C 3 HOH A 35 435 2046 HOH HOH . C 3 HOH A 36 436 2126 HOH HOH . C 3 HOH A 37 437 2026 HOH HOH . C 3 HOH A 38 438 2038 HOH HOH . C 3 HOH A 39 439 2083 HOH HOH . C 3 HOH A 40 440 2055 HOH HOH . C 3 HOH A 41 441 2014 HOH HOH . C 3 HOH A 42 442 2094 HOH HOH . C 3 HOH A 43 443 2019 HOH HOH . C 3 HOH A 44 444 2119 HOH HOH . C 3 HOH A 45 445 2098 HOH HOH . C 3 HOH A 46 446 2011 HOH HOH . C 3 HOH A 47 447 2089 HOH HOH . C 3 HOH A 48 448 2088 HOH HOH . C 3 HOH A 49 449 2092 HOH HOH . C 3 HOH A 50 450 2062 HOH HOH . C 3 HOH A 51 451 2116 HOH HOH . C 3 HOH A 52 452 2030 HOH HOH . C 3 HOH A 53 453 2063 HOH HOH . C 3 HOH A 54 454 2111 HOH HOH . C 3 HOH A 55 455 2105 HOH HOH . C 3 HOH A 56 456 2104 HOH HOH . C 3 HOH A 57 457 2002 HOH HOH . C 3 HOH A 58 458 2099 HOH HOH . C 3 HOH A 59 459 2061 HOH HOH . C 3 HOH A 60 460 2121 HOH HOH . C 3 HOH A 61 461 2120 HOH HOH . C 3 HOH A 62 462 2021 HOH HOH . C 3 HOH A 63 463 2044 HOH HOH . C 3 HOH A 64 464 2108 HOH HOH . C 3 HOH A 65 465 2013 HOH HOH . C 3 HOH A 66 466 2096 HOH HOH . C 3 HOH A 67 467 2087 HOH HOH . C 3 HOH A 68 468 2004 HOH HOH . C 3 HOH A 69 469 2041 HOH HOH . C 3 HOH A 70 470 2107 HOH HOH . C 3 HOH A 71 471 2091 HOH HOH . C 3 HOH A 72 472 2060 HOH HOH . C 3 HOH A 73 473 2010 HOH HOH . C 3 HOH A 74 474 2036 HOH HOH . C 3 HOH A 75 475 2040 HOH HOH . C 3 HOH A 76 476 2118 HOH HOH . C 3 HOH A 77 477 2103 HOH HOH . C 3 HOH A 78 478 2048 HOH HOH . C 3 HOH A 79 479 2023 HOH HOH . C 3 HOH A 80 480 2017 HOH HOH . C 3 HOH A 81 481 2047 HOH HOH . C 3 HOH A 82 482 2042 HOH HOH . C 3 HOH A 83 483 2071 HOH HOH . C 3 HOH A 84 484 2072 HOH HOH . C 3 HOH A 85 485 2114 HOH HOH . C 3 HOH A 86 486 2006 HOH HOH . C 3 HOH A 87 487 2115 HOH HOH . C 3 HOH A 88 488 2057 HOH HOH . C 3 HOH A 89 489 2125 HOH HOH . C 3 HOH A 90 490 2035 HOH HOH . C 3 HOH A 91 491 2095 HOH HOH . C 3 HOH A 92 492 2027 HOH HOH . C 3 HOH A 93 493 2045 HOH HOH . C 3 HOH A 94 494 2031 HOH HOH . C 3 HOH A 95 495 2020 HOH HOH . C 3 HOH A 96 496 2109 HOH HOH . C 3 HOH A 97 497 2097 HOH HOH . C 3 HOH A 98 498 2025 HOH HOH . C 3 HOH A 99 499 2007 HOH HOH . C 3 HOH A 100 500 2029 HOH HOH . C 3 HOH A 101 501 2124 HOH HOH . C 3 HOH A 102 502 2122 HOH HOH . C 3 HOH A 103 503 2064 HOH HOH . C 3 HOH A 104 504 2101 HOH HOH . C 3 HOH A 105 505 2102 HOH HOH . C 3 HOH A 106 506 2016 HOH HOH . C 3 HOH A 107 507 2082 HOH HOH . C 3 HOH A 108 508 2074 HOH HOH . C 3 HOH A 109 509 2112 HOH HOH . C 3 HOH A 110 510 2075 HOH HOH . C 3 HOH A 111 511 2084 HOH HOH . C 3 HOH A 112 512 2039 HOH HOH . C 3 HOH A 113 513 2032 HOH HOH . C 3 HOH A 114 514 2050 HOH HOH . C 3 HOH A 115 515 2008 HOH HOH . C 3 HOH A 116 516 2056 HOH HOH . C 3 HOH A 117 517 2051 HOH HOH . C 3 HOH A 118 518 2018 HOH HOH . C 3 HOH A 119 519 2085 HOH HOH . C 3 HOH A 120 520 2081 HOH HOH . C 3 HOH A 121 521 2079 HOH HOH . C 3 HOH A 122 522 2034 HOH HOH . C 3 HOH A 123 523 2053 HOH HOH . C 3 HOH A 124 524 2070 HOH HOH . C 3 HOH A 125 525 2058 HOH HOH . C 3 HOH A 126 526 2015 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 4K4 . . . B 2 4.565 -4.807 18.825 1 31.35 ? C4 4K4 301 A 1 HETATM 2 C C5 4K4 . . . B 2 5.593 -3.828 18.915 1 33.16 ? C5 4K4 301 A 1 HETATM 3 C C6 4K4 . . . B 2 5.354 -2.626 19.605 1 32.14 ? C6 4K4 301 A 1 HETATM 4 N N1 4K4 . . . B 2 4.158 -2.481 20.156 1 33.1 ? N1 4K4 301 A 1 HETATM 5 N N3 4K4 . . . B 2 3.397 -4.606 19.41 1 33.18 ? N3 4K4 301 A 1 HETATM 6 C CAU 4K4 . . . B 2 -3.112 -11.221 24.114 1 105.68 ? CAU 4K4 301 A 1 HETATM 7 C CAS 4K4 . . . B 2 -2.952 -12.74 24.402 1 105.99 ? CAS 4K4 301 A 1 HETATM 8 N NBL 4K4 . . . B 2 -4.225 -13.483 24.209 1 109.55 ? NBL 4K4 301 A 1 HETATM 9 C CAB 4K4 . . . B 2 -4.021 -14.943 24.335 1 102.87 ? CAB 4K4 301 A 1 HETATM 10 C CAT 4K4 . . . B 2 -4.93 -13.152 22.937 1 108.83 ? CAT 4K4 301 A 1 HETATM 11 C CAV 4K4 . . . B 2 -5.009 -11.632 22.638 1 104.17 ? CAV 4K4 301 A 1 HETATM 12 N NBN 4K4 . . . B 2 -3.683 -11.006 22.739 1 102.9 ? NBN 4K4 301 A 1 HETATM 13 C CBK 4K4 . . . B 2 -3.535 -9.715 21.996 1 89.26 ? CBK 4K4 301 A 1 HETATM 14 C CAP 4K4 . . . B 2 -4.739 -8.736 22.075 1 78.77 ? CAP 4K4 301 A 1 HETATM 15 C CAR 4K4 . . . B 2 -4.556 -7.56 21.155 1 70.94 ? CAR 4K4 301 A 1 HETATM 16 C CAO 4K4 . . . B 2 -2.321 -8.958 22.489 1 84.46 ? CAO 4K4 301 A 1 HETATM 17 C CAQ 4K4 . . . B 2 -1.992 -7.765 21.613 1 77.78 ? CAQ 4K4 301 A 1 HETATM 18 N NBM 4K4 . . . B 2 -3.175 -6.972 21.144 1 68.59 ? NBM 4K4 301 A 1 HETATM 19 C CBA 4K4 . . . B 2 -2.997 -5.699 20.705 1 57.67 ? CBA 4K4 301 A 1 HETATM 20 O OAE 4K4 . . . B 2 -3.976 -4.994 20.52 1 52.73 ? OAE 4K4 301 A 1 HETATM 21 C CBB 4K4 . . . B 2 -1.73 -5.091 20.634 1 48.88 ? CBB 4K4 301 A 1 HETATM 22 C CAN 4K4 . . . B 2 -1.376 -4.227 21.656 1 44.88 ? CAN 4K4 301 A 1 HETATM 23 C CBE 4K4 . . . B 2 -0.127 -3.619 21.634 1 46.97 ? CBE 4K4 301 A 1 HETATM 24 O OAZ 4K4 . . . B 2 0.351 -2.754 22.588 1 49.35 ? OAZ 4K4 301 A 1 HETATM 25 C CAA 4K4 . . . B 2 -0.12 -2.94 23.926 1 44.7 ? CAA 4K4 301 A 1 HETATM 26 C CAI 4K4 . . . B 2 -0.825 -5.333 19.6 1 45.33 ? CAI 4K4 301 A 1 HETATM 27 C CAJ 4K4 . . . B 2 0.438 -4.725 19.573 1 45.42 ? CAJ 4K4 301 A 1 HETATM 28 C CBC 4K4 . . . B 2 0.801 -3.847 20.611 1 42.64 ? CBC 4K4 301 A 1 HETATM 29 N NAY 4K4 . . . B 2 2.009 -3.144 20.698 1 36.85 ? NAY 4K4 301 A 1 HETATM 30 C C2 4K4 . . . B 2 3.219 -3.45 20.066 1 33.29 ? C2 4K4 301 A 1 HETATM 31 N NBP 4K4 . . . B 2 4.7 -5.927 18.161 1 31.04 ? NBP 4K4 301 A 1 HETATM 32 C CAD 4K4 . . . B 2 3.793 -7.018 18.518 1 34.58 ? CAD 4K4 301 A 1 HETATM 33 C CBH 4K4 . . . B 2 5.012 -5.87 16.778 1 31.96 ? CBH 4K4 301 A 1 HETATM 34 C CAL 4K4 . . . B 2 4.113 -6.379 15.821 1 30.17 ? CAL 4K4 301 A 1 HETATM 35 C CAH 4K4 . . . B 2 4.424 -6.369 14.469 1 29.89 ? CAH 4K4 301 A 1 HETATM 36 C CAG 4K4 . . . B 2 5.62 -5.813 14.019 1 28.08 ? CAG 4K4 301 A 1 HETATM 37 C CAK 4K4 . . . B 2 6.504 -5.254 14.93 1 28.6 ? CAK 4K4 301 A 1 HETATM 38 C CBG 4K4 . . . B 2 6.205 -5.309 16.306 1 30.79 ? CBG 4K4 301 A 1 HETATM 39 C CBF 4K4 . . . B 2 7.188 -4.734 17.242 1 33 ? CBF 4K4 301 A 1 HETATM 40 O OAF 4K4 . . . B 2 8.373 -4.918 16.94 1 34.21 ? OAF 4K4 301 A 1 HETATM 41 N NBO 4K4 . . . B 2 6.868 -4.011 18.355 1 35.54 ? NBO 4K4 301 A 1 HETATM 42 C CAC 4K4 . . . B 2 7.989 -3.377 19.055 1 36.1 ? CAC 4K4 301 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 42 #