data_5PZO # _model_server_result.job_id k3KPBvsG4MUoqv3cnYgDOQ _model_server_result.datetime_utc '2025-08-15 17:24:06' _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 5pzo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":601}' # _entry.id 5PZO # _exptl.entry_id 5PZO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 630.732 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid' _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 90 _cell.angle_gamma 90 _cell.entry_id 5PZO _cell.length_a 65.2 _cell.length_b 90.3 _cell.length_c 234.9 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5PZO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,M,X 1 1 B,N,O,P,Q,R,S,T,U,V,W,Y 2 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 N N N # _chem_comp.formula 'C38 H38 N4 O5' _chem_comp.formula_weight 630.732 _chem_comp.id 23E _chem_comp.mon_nstd_flag . _chem_comp.name '(2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic 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 C2 N1 23E sing 1 n n N1 C21 23E sing 2 n n N1 HN1 23E sing 3 n n C17 C2 23E sing 4 n n C3 C2 23E sing 5 n n C16 C2 23E sing 6 n n O6 C3 23E doub 7 n n C3 N4 23E sing 8 n n C5 N4 23E sing 9 n n N4 HN4 23E sing 10 n n C7 C5 23E doub 11 n y C11 C5 23E sing 12 n y C8 C7 23E sing 13 n y C7 H7 23E sing 14 n n C9 C8 23E doub 15 n y C8 H8 23E sing 16 n n C12 C9 23E sing 17 n n C9 C10 23E sing 18 n y C10 C11 23E doub 19 n y C10 H10 23E sing 20 e n C11 H11 23E sing 21 n n C12 C13 23E doub 22 n n C12 H12 23E sing 23 n n C14 C13 23E sing 24 n n C13 H13 23E sing 25 n n O15 C14 23E doub 26 n n C14 O20 23E sing 27 n n C18 C16 23E sing 28 n n C16 H16 23E sing 29 n n C16 H16A 23E sing 30 n n C19 C17 23E sing 31 n n C17 H17 23E sing 32 n n C17 H17A 23E sing 33 n n C19 C18 23E sing 34 n n C18 H18 23E sing 35 n n C18 H18A 23E sing 36 n n C19 H19 23E sing 37 n n C19 H19A 23E sing 38 n n O20 HO20 23E sing 39 n n O38 C21 23E doub 40 n n C21 C22 23E sing 41 n n C22 C25 23E doub 42 n y C22 C23 23E sing 43 n y C23 C24 23E doub 44 n y C23 H23 23E sing 45 n n C24 C28 23E sing 46 n y C24 H24 23E sing 47 n n C25 C27 23E sing 48 n y C25 H25 23E sing 49 n n C44 N26 23E sing 50 n n C27 N26 23E sing 51 n y N26 C30 23E sing 52 n y C27 C28 23E doub 53 n y C28 C29 23E sing 54 n y C30 C29 23E doub 55 n y C29 C31 23E sing 56 n n C30 C32 23E sing 57 n y C31 C37 23E sing 58 n n C31 C33 23E sing 59 n n C31 H31 23E sing 60 n n C43 C32 23E doub 61 n y C32 C39 23E sing 62 n y C33 C34 23E sing 63 n n C33 H33 23E sing 64 n n C33 H33A 23E sing 65 n n C35 C34 23E sing 66 n n C34 H34 23E sing 67 n n C34 H34A 23E sing 68 n n C36 C35 23E sing 69 n n C35 H35 23E sing 70 n n C35 H35A 23E sing 71 n n C37 C36 23E sing 72 n n C36 H36 23E sing 73 n n C36 H36A 23E sing 74 n n C37 H37 23E sing 75 n n C37 H37A 23E sing 76 n n C39 C40 23E doub 77 n y C39 H39 23E sing 78 n n C41 C40 23E sing 79 n y C40 H40 23E sing 80 n n C42 C41 23E doub 81 n y C41 H41 23E sing 82 n n C43 C42 23E sing 83 n y C42 H42 23E sing 84 n n N45 C43 23E sing 85 n n C44 C46 23E sing 86 n n C44 H44 23E sing 87 n n C44 H44A 23E sing 88 n n C46 N45 23E sing 89 n n N45 HN45 23E sing 90 n n O47 C46 23E doub 91 n n # _atom_sites.entry_id 5PZO _atom_sites.fract_transf_matrix[1][1] 0.015337 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011074 _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] 0.004257 _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 23E A 1 601 601 23E 23E . D 3 8XM A 1 602 602 8XM LG1 . E 4 SO4 A 1 603 1 SO4 SO4 . F 4 SO4 A 1 604 3 SO4 SO4 . G 4 SO4 A 1 605 4 SO4 SO4 . H 4 SO4 A 1 606 6 SO4 SO4 . I 5 GOL A 1 607 21 GOL GOL . J 5 GOL A 1 608 22 GOL GOL . K 5 GOL A 1 609 23 GOL GOL . L 5 GOL A 1 610 27 GOL GOL . M 5 GOL A 1 611 31 GOL GOL . N 2 23E B 1 601 601 23E 23E . O 3 8XM B 1 602 602 8XM LG1 . P 4 SO4 B 1 603 5 SO4 SO4 . Q 4 SO4 B 1 604 7 SO4 SO4 . R 4 SO4 B 1 605 9 SO4 SO4 . S 4 SO4 B 1 606 12 SO4 SO4 . T 5 GOL B 1 607 24 GOL GOL . U 5 GOL B 1 608 25 GOL GOL . V 5 GOL B 1 609 30 GOL GOL . W 5 GOL B 1 610 33 GOL GOL . X 6 HOH A 1 701 21 HOH HOH . X 6 HOH A 2 702 24 HOH HOH . X 6 HOH A 3 703 25 HOH HOH . X 6 HOH A 4 704 23 HOH HOH . X 6 HOH A 5 705 47 HOH HOH . X 6 HOH A 6 706 35 HOH HOH . X 6 HOH A 7 707 32 HOH HOH . X 6 HOH A 8 708 30 HOH HOH . X 6 HOH A 9 709 15 HOH HOH . X 6 HOH A 10 710 10 HOH HOH . X 6 HOH A 11 711 51 HOH HOH . X 6 HOH A 12 712 31 HOH HOH . X 6 HOH A 13 713 20 HOH HOH . X 6 HOH A 14 714 42 HOH HOH . X 6 HOH A 15 715 29 HOH HOH . X 6 HOH A 16 716 48 HOH HOH . X 6 HOH A 17 717 3 HOH HOH . X 6 HOH A 18 718 8 HOH HOH . X 6 HOH A 19 719 53 HOH HOH . X 6 HOH A 20 720 4 HOH HOH . X 6 HOH A 21 721 17 HOH HOH . X 6 HOH A 22 722 12 HOH HOH . X 6 HOH A 23 723 37 HOH HOH . X 6 HOH A 24 724 11 HOH HOH . X 6 HOH A 25 725 43 HOH HOH . X 6 HOH A 26 726 54 HOH HOH . X 6 HOH A 27 727 41 HOH HOH . X 6 HOH A 28 728 19 HOH HOH . X 6 HOH A 29 729 50 HOH HOH . X 6 HOH A 30 730 28 HOH HOH . X 6 HOH A 31 731 6 HOH HOH . X 6 HOH A 32 732 44 HOH HOH . X 6 HOH A 33 733 13 HOH HOH . X 6 HOH A 34 734 18 HOH HOH . X 6 HOH A 35 735 16 HOH HOH . X 6 HOH A 36 736 49 HOH HOH . X 6 HOH A 37 737 26 HOH HOH . X 6 HOH A 38 738 56 HOH HOH . X 6 HOH A 39 739 45 HOH HOH . Y 6 HOH B 1 701 22 HOH HOH . Y 6 HOH B 2 702 40 HOH HOH . Y 6 HOH B 3 703 34 HOH HOH . Y 6 HOH B 4 704 1 HOH HOH . Y 6 HOH B 5 705 36 HOH HOH . Y 6 HOH B 6 706 2 HOH HOH . Y 6 HOH B 7 707 55 HOH HOH . Y 6 HOH B 8 708 39 HOH HOH . Y 6 HOH B 9 709 46 HOH HOH . Y 6 HOH B 10 710 5 HOH HOH . Y 6 HOH B 11 711 14 HOH HOH . Y 6 HOH B 12 712 38 HOH HOH . Y 6 HOH B 13 713 27 HOH HOH . Y 6 HOH B 14 714 33 HOH HOH . Y 6 HOH B 15 715 7 HOH HOH . Y 6 HOH B 16 716 52 HOH HOH . Y 6 HOH B 17 717 9 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 N1 23E . . . N 2 13.42 1.114 103.795 1 45.5 ? N1 23E 601 B 1 HETATM 2 C C2 23E . . . N 2 13.516 1.066 105.253 1 44.48 ? C2 23E 601 B 1 HETATM 3 C C3 23E . . . N 2 14.2 2.334 105.851 1 44.89 ? C3 23E 601 B 1 HETATM 4 N N4 23E . . . N 2 13.692 3.521 105.447 1 46.73 ? N4 23E 601 B 1 HETATM 5 C C5 23E . . . N 2 14.001 4.819 105.922 1 46.79 ? C5 23E 601 B 1 HETATM 6 O O6 23E . . . N 2 15.094 2.229 106.671 1 44.21 ? O6 23E 601 B 1 HETATM 7 C C7 23E . . . N 2 15.182 5.125 106.596 1 45.84 ? C7 23E 601 B 1 HETATM 8 C C8 23E . . . N 2 15.44 6.425 106.991 1 50.88 ? C8 23E 601 B 1 HETATM 9 C C9 23E . . . N 2 14.534 7.462 106.726 1 55.26 ? C9 23E 601 B 1 HETATM 10 C C10 23E . . . N 2 13.361 7.141 106.033 1 47.96 ? C10 23E 601 B 1 HETATM 11 C C11 23E . . . N 2 13.092 5.84 105.642 1 45.3 ? C11 23E 601 B 1 HETATM 12 C C12 23E . . . N 2 14.789 8.847 107.157 1 62.49 ? C12 23E 601 B 1 HETATM 13 C C13 23E . . . N 2 15.85 9.305 107.833 1 69.6 ? C13 23E 601 B 1 HETATM 14 C C14 23E . . . N 2 15.982 10.672 108.409 1 76.84 ? C14 23E 601 B 1 HETATM 15 O O15 23E . . . N 2 17.054 10.944 108.955 1 77.94 ? O15 23E 601 B 1 HETATM 16 C C16 23E . . . N 2 14.184 -0.249 105.699 1 41.06 ? C16 23E 601 B 1 HETATM 17 C C17 23E . . . N 2 12.12 0.923 105.882 1 42.03 ? C17 23E 601 B 1 HETATM 18 C C18 23E . . . N 2 13.642 -0.481 107.106 1 39.63 ? C18 23E 601 B 1 HETATM 19 C C19 23E . . . N 2 12.427 0.432 107.269 1 40.12 ? C19 23E 601 B 1 HETATM 20 O O20 23E . . . N 2 14.996 11.547 108.333 1 79.65 ? O20 23E 601 B 1 HETATM 21 C C21 23E . . . N 2 14.424 1.544 102.997 1 48.34 ? C21 23E 601 B 1 HETATM 22 C C22 23E . . . N 2 14.094 1.705 101.542 1 49.07 ? C22 23E 601 B 1 HETATM 23 C C23 23E . . . N 2 15.09 1.444 100.601 1 48.46 ? C23 23E 601 B 1 HETATM 24 C C24 23E . . . N 2 14.807 1.436 99.247 1 48.6 ? C24 23E 601 B 1 HETATM 25 C C25 23E . . . N 2 12.802 2.021 101.113 1 47.15 ? C25 23E 601 B 1 HETATM 26 N N26 23E . . . N 2 11.328 2.204 99.069 1 50.63 ? N26 23E 601 B 1 HETATM 27 C C27 23E . . . N 2 12.528 1.994 99.75 1 48.22 ? C27 23E 601 B 1 HETATM 28 C C28 23E . . . N 2 13.51 1.675 98.803 1 48.36 ? C28 23E 601 B 1 HETATM 29 C C29 23E . . . N 2 12.866 1.659 97.509 1 47.24 ? C29 23E 601 B 1 HETATM 30 C C30 23E . . . N 2 11.54 1.978 97.717 1 50.58 ? C30 23E 601 B 1 HETATM 31 C C31 23E . . . N 2 13.539 1.382 96.194 1 42.08 ? C31 23E 601 B 1 HETATM 32 C C32 23E . . . N 2 10.381 2.02 96.807 1 54.95 ? C32 23E 601 B 1 HETATM 33 C C33 23E . . . N 2 14.538 2.486 95.816 1 43.98 ? C33 23E 601 B 1 HETATM 34 C C34 23E . . . N 2 15.168 2.237 94.447 1 43.33 ? C34 23E 601 B 1 HETATM 35 C C35 23E . . . N 2 15.843 0.881 94.399 1 43.68 ? C35 23E 601 B 1 HETATM 36 C C36 23E . . . N 2 14.86 -0.224 94.768 1 42.81 ? C36 23E 601 B 1 HETATM 37 C C37 23E . . . N 2 14.236 0.02 96.142 1 40.4 ? C37 23E 601 B 1 HETATM 38 O O38 23E . . . N 2 15.564 1.763 103.422 1 44.7 ? O38 23E 601 B 1 HETATM 39 C C39 23E . . . N 2 10.469 2.707 95.591 1 56.02 ? C39 23E 601 B 1 HETATM 40 C C40 23E . . . N 2 9.406 2.705 94.702 1 55.6 ? C40 23E 601 B 1 HETATM 41 C C41 23E . . . N 2 8.25 2.013 95 1 56.59 ? C41 23E 601 B 1 HETATM 42 C C42 23E . . . N 2 8.136 1.322 96.198 1 58.2 ? C42 23E 601 B 1 HETATM 43 C C43 23E . . . N 2 9.187 1.329 97.12 1 55.66 ? C43 23E 601 B 1 HETATM 44 C C44 23E . . . N 2 10.035 2.511 99.679 1 51.27 ? C44 23E 601 B 1 HETATM 45 N N45 23E . . . N 2 8.972 0.673 98.357 1 51.46 ? N45 23E 601 B 1 HETATM 46 C C46 23E . . . N 2 9.315 1.139 99.581 1 53.58 ? C46 23E 601 B 1 HETATM 47 O O47 23E . . . N 2 9.09 0.483 100.594 1 53.82 ? O47 23E 601 B 1 HETATM 48 H HN1 23E . . . N 2 12.556 0.748 103.411 0 45.4 ? HN1 23E 601 B 1 HETATM 49 H HN4 23E . . . N 2 12.999 3.524 104.705 0 46.63 ? HN4 23E 601 B 1 HETATM 50 H H7 23E . . . N 2 15.945 4.378 106.801 0 45.76 ? H7 23E 601 B 1 HETATM 51 H H8 23E . . . N 2 16.388 6.618 107.488 0 50.9 ? H8 23E 601 B 1 HETATM 52 H H10 23E . . . N 2 12.634 7.915 105.794 0 47.92 ? H10 23E 601 B 1 HETATM 53 H H11 23E . . . N 2 12.154 5.648 105.123 0 45.1 ? H11 23E 601 B 1 HETATM 54 H H12 23E . . . N 2 14.008 9.531 106.828 0 62.46 ? H12 23E 601 B 1 HETATM 55 H H13 23E . . . N 2 16.723 8.682 108.016 0 69.6 ? H13 23E 601 B 1 HETATM 56 H H16 23E . . . N 2 13.981 -1.094 105.043 0 41.08 ? H16 23E 601 B 1 HETATM 57 H H16A 23E . . . N 2 15.271 -0.185 105.676 0 41.08 ? H16A 23E 601 B 1 HETATM 58 H H17 23E . . . N 2 11.507 0.188 105.363 0 42.09 ? H17 23E 601 B 1 HETATM 59 H H17A 23E . . . N 2 11.553 1.851 105.84 0 42.09 ? H17A 23E 601 B 1 HETATM 60 H H18 23E . . . N 2 14.402 -0.344 107.874 0 39.69 ? H18 23E 601 B 1 HETATM 61 H H18A 23E . . . N 2 13.356 -1.525 107.218 0 39.69 ? H18A 23E 601 B 1 HETATM 62 H H19 23E . . . N 2 12.582 1.241 107.982 0 40.16 ? H19 23E 601 B 1 HETATM 63 H H19A 23E . . . N 2 11.575 -0.106 107.676 0 40.16 ? H19A 23E 601 B 1 HETATM 64 H HO20 23E . . . N 2 14.167 11.231 107.889 0 79.58 ? HO20 23E 601 B 1 HETATM 65 H H23 23E . . . N 2 16.118 1.238 100.896 0 48.54 ? H23 23E 601 B 1 HETATM 66 H H24 23E . . . N 2 15.617 1.272 98.539 0 48.68 ? H24 23E 601 B 1 HETATM 67 H H25 23E . . . N 2 12.042 2.311 101.838 0 47.35 ? H25 23E 601 B 1 HETATM 68 H H31 23E . . . N 2 12.774 1.353 95.421 0 42.08 ? H31 23E 601 B 1 HETATM 69 H H33 23E . . . N 2 14.055 3.462 95.844 0 44.03 ? H33 23E 601 B 1 HETATM 70 H H33A 23E . . . N 2 15.325 2.55 96.567 0 44.03 ? H33A 23E 601 B 1 HETATM 71 H H34 23E . . . N 2 14.411 2.309 93.668 0 43.33 ? H34 23E 601 B 1 HETATM 72 H H34A 23E . . . N 2 15.874 3.023 94.185 0 43.33 ? H34A 23E 601 B 1 HETATM 73 H H35 23E . . . N 2 16.277 0.696 93.418 0 43.68 ? H35 23E 601 B 1 HETATM 74 H H35A 23E . . . N 2 16.685 0.866 95.089 0 43.68 ? H35A 23E 601 B 1 HETATM 75 H H36 23E . . . N 2 14.074 -0.26 94.018 0 42.79 ? H36 23E 601 B 1 HETATM 76 H H36A 23E . . . N 2 15.331 -1.205 94.724 0 42.79 ? H36A 23E 601 B 1 HETATM 77 H H37 23E . . . N 2 15.018 -0.057 96.895 0 40.37 ? H37 23E 601 B 1 HETATM 78 H H37A 23E . . . N 2 13.53 -0.771 96.391 0 40.37 ? H37A 23E 601 B 1 HETATM 79 H H39 23E . . . N 2 11.387 3.236 95.341 0 55.95 ? H39 23E 601 B 1 HETATM 80 H H40 23E . . . N 2 9.492 3.255 93.766 0 55.55 ? H40 23E 601 B 1 HETATM 81 H H41 23E . . . N 2 7.42 2.009 94.294 0 56.54 ? H41 23E 601 B 1 HETATM 82 H H42 23E . . . N 2 7.216 0.775 96.402 0 58.22 ? H42 23E 601 B 1 HETATM 83 H H44 23E . . . N 2 10.127 2.82 100.718 0 51.24 ? H44 23E 601 B 1 HETATM 84 H H44A 23E . . . N 2 9.513 3.317 99.17 0 51.24 ? H44A 23E 601 B 1 HETATM 85 H HN45 23E . . . N 2 8.517 -0.232 98.305 0 51.53 ? HN45 23E 601 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 85 #