data_9BXY # _model_server_result.job_id XE2bwSvO8ybTa7wkAHhaFw _model_server_result.datetime_utc '2025-07-07 17:19:20' _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 9bxy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":511}' # _entry.id 9BXY # _exptl.entry_id 9BXY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 538.015 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,5R)-1-[4-(1-carbamimidoyl-L-prolyl)piperazine-1-carbonyl]-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)piperidine-3-carboxamide _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 90 _cell.entry_id 9BXY _cell.length_a 66.467 _cell.length_b 67.686 _cell.length_c 87.389 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BXY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,G,H,I,J,K,L,M _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 L _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 13 A CYS 54 1_555 A SG CYS 33 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale8 A ND2 ASN 255 A ASN 386 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 A ND2 ASN 311 A ASN 448 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? # _chem_comp.formula 'C24 H33 Cl F N7 O4' _chem_comp.formula_weight 538.015 _chem_comp.id A1ATE _chem_comp.mon_nstd_flag . _chem_comp.name (3S,5R)-1-[4-(1-carbamimidoyl-L-prolyl)piperazine-1-carbonyl]-N-(4-chloro-3-fluorophenyl)-5-(hydroxymethyl)piperidine-3-carboxamide _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 CL1 C17 A1ATE sing 1 n n C19 C17 A1ATE doub 2 n y C19 C20 A1ATE sing 3 n y C17 C15 A1ATE sing 4 n y C20 C13 A1ATE doub 5 n y C15 F16 A1ATE sing 6 n n C15 C14 A1ATE doub 7 n y C13 C14 A1ATE sing 8 n y C13 N12 A1ATE sing 9 n n N12 C10 A1ATE sing 10 n n C10 O11 A1ATE doub 11 n n C10 C09 A1ATE sing 12 n n C21 C09 A1ATE sing 13 n n C21 C22 A1ATE sing 14 n n C09 C08 A1ATE sing 15 n n C22 C27 A1ATE sing 16 n n C22 C23 A1ATE sing 17 n n C27 O28 A1ATE sing 18 n n C08 N07 A1ATE sing 19 n n N07 C23 A1ATE sing 20 n n N07 C06 A1ATE sing 21 n n C25 N05 A1ATE sing 22 n n C25 C26 A1ATE sing 23 n n C06 N05 A1ATE sing 24 n n C06 O24 A1ATE doub 25 n n N05 C04 A1ATE sing 26 n n C04 C03 A1ATE sing 27 n n C26 N02 A1ATE sing 28 n n C03 N02 A1ATE sing 29 n n N02 C01 A1ATE sing 30 n n NH1 CZ A1ATE doub 31 n n C01 O27 A1ATE doub 32 n n C01 CG A1ATE sing 33 n n CZ NH2 A1ATE sing 34 n n CZ ND1 A1ATE sing 35 n n CG ND1 A1ATE sing 36 n n CG CD2 A1ATE sing 37 n n ND1 CE2 A1ATE sing 38 n n CD2 CE1 A1ATE sing 39 n n CE2 CE1 A1ATE sing 40 n n CG H1 A1ATE sing 41 n n CD2 H2 A1ATE sing 42 n n CD2 H3 A1ATE sing 43 n n CE1 H4 A1ATE sing 44 n n CE1 H5 A1ATE sing 45 n n CE2 H6 A1ATE sing 46 n n CE2 H7 A1ATE sing 47 n n NH1 H8 A1ATE sing 48 n n NH2 H9 A1ATE sing 49 n n NH2 H10 A1ATE sing 50 n n C03 H11 A1ATE sing 51 n n C03 H12 A1ATE sing 52 n n C04 H13 A1ATE sing 53 n n C04 H14 A1ATE sing 54 n n C08 H15 A1ATE sing 55 n n C08 H16 A1ATE sing 56 n n C09 H17 A1ATE sing 57 n n C14 H18 A1ATE sing 58 n n C19 H19 A1ATE sing 59 n n C20 H20 A1ATE sing 60 n n C21 H21 A1ATE sing 61 n n C21 H22 A1ATE sing 62 n n C22 H23 A1ATE sing 63 n n C23 H24 A1ATE sing 64 n n C23 H25 A1ATE sing 65 n n C25 H26 A1ATE sing 66 n n C25 H27 A1ATE sing 67 n n C26 H28 A1ATE sing 68 n n C26 H29 A1ATE sing 69 n n C27 H30 A1ATE sing 70 n n C27 H31 A1ATE sing 71 n n N12 H32 A1ATE sing 72 n n O28 H33 A1ATE sing 73 n n # _atom_sites.entry_id 9BXY _atom_sites.fract_transf_matrix[1][1] 0.015045 _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] 0.014774 _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] 0.011443 _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 NAG A 1 501 501 NAG NAG . C 2 NAG A 1 502 502 NAG NAG . D 2 NAG A 1 503 503 NAG NAG . E 2 NAG A 1 504 504 NAG NAG . F 2 NAG A 1 505 505 NAG NAG . G 2 NAG A 1 506 506 NAG NAG . H 2 NAG A 1 507 507 NAG NAG . I 2 NAG A 1 508 508 NAG NAG . J 2 NAG A 1 509 510 NAG NAG . K 3 EPE A 1 510 512 EPE EPE . L 4 A1ATE A 1 511 1 A1ATE MW5 . M 5 HOH A 1 601 17 HOH HOH . M 5 HOH A 2 602 21 HOH HOH . M 5 HOH A 3 603 43 HOH HOH . M 5 HOH A 4 604 75 HOH HOH . M 5 HOH A 5 605 41 HOH HOH . M 5 HOH A 6 606 15 HOH HOH . M 5 HOH A 7 607 53 HOH HOH . M 5 HOH A 8 608 6 HOH HOH . M 5 HOH A 9 609 29 HOH HOH . M 5 HOH A 10 610 7 HOH HOH . M 5 HOH A 11 611 10 HOH HOH . M 5 HOH A 12 612 32 HOH HOH . M 5 HOH A 13 613 8 HOH HOH . M 5 HOH A 14 614 50 HOH HOH . M 5 HOH A 15 615 5 HOH HOH . M 5 HOH A 16 616 25 HOH HOH . M 5 HOH A 17 617 19 HOH HOH . M 5 HOH A 18 618 73 HOH HOH . M 5 HOH A 19 619 46 HOH HOH . M 5 HOH A 20 620 37 HOH HOH . M 5 HOH A 21 621 55 HOH HOH . M 5 HOH A 22 622 38 HOH HOH . M 5 HOH A 23 623 70 HOH HOH . M 5 HOH A 24 624 12 HOH HOH . M 5 HOH A 25 625 1 HOH HOH . M 5 HOH A 26 626 11 HOH HOH . M 5 HOH A 27 627 9 HOH HOH . M 5 HOH A 28 628 26 HOH HOH . M 5 HOH A 29 629 24 HOH HOH . M 5 HOH A 30 630 16 HOH HOH . M 5 HOH A 31 631 13 HOH HOH . M 5 HOH A 32 632 28 HOH HOH . M 5 HOH A 33 633 33 HOH HOH . M 5 HOH A 34 634 47 HOH HOH . M 5 HOH A 35 635 30 HOH HOH . M 5 HOH A 36 636 31 HOH HOH . M 5 HOH A 37 637 14 HOH HOH . M 5 HOH A 38 638 2 HOH HOH . M 5 HOH A 39 639 27 HOH HOH . M 5 HOH A 40 640 54 HOH HOH . M 5 HOH A 41 641 52 HOH HOH . M 5 HOH A 42 642 64 HOH HOH . M 5 HOH A 43 643 71 HOH HOH . M 5 HOH A 44 644 4 HOH HOH . M 5 HOH A 45 645 39 HOH HOH . M 5 HOH A 46 646 76 HOH HOH . M 5 HOH A 47 647 3 HOH HOH . M 5 HOH A 48 648 23 HOH HOH . M 5 HOH A 49 649 34 HOH HOH . M 5 HOH A 50 650 51 HOH HOH . M 5 HOH A 51 651 40 HOH HOH . M 5 HOH A 52 652 62 HOH HOH . M 5 HOH A 53 653 35 HOH HOH . M 5 HOH A 54 654 48 HOH HOH . M 5 HOH A 55 655 72 HOH HOH . M 5 HOH A 56 656 18 HOH HOH . M 5 HOH A 57 657 36 HOH HOH . M 5 HOH A 58 658 74 HOH HOH . M 5 HOH A 59 659 58 HOH HOH . M 5 HOH A 60 660 56 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 C10 A1ATE . . . L 4 -4.126 15.987 -13.914 1 40.78 ? C10 A1ATE 511 A 1 HETATM 2 C CG A1ATE . . . L 4 -2.512 10.42 -6.751 1 78.01 ? CG A1ATE 511 A 1 HETATM 3 N ND1 A1ATE . . . L 4 -2.527 9.137 -6.481 1 82.75 ? ND1 A1ATE 511 A 1 HETATM 4 C CD2 A1ATE . . . L 4 -2.631 11.259 -5.328 1 73.75 ? CD2 A1ATE 511 A 1 HETATM 5 C CE1 A1ATE . . . L 4 -3.033 10.436 -4.417 1 71.7 ? CE1 A1ATE 511 A 1 HETATM 6 C CE2 A1ATE . . . L 4 -2.502 9.064 -4.9 1 71.65 ? CE2 A1ATE 511 A 1 HETATM 7 C CZ A1ATE . . . L 4 -2.535 7.975 -7.408 1 84.43 ? CZ A1ATE 511 A 1 HETATM 8 N NH1 A1ATE . . . L 4 -2.549 8.097 -8.67 1 77.45 ? NH1 A1ATE 511 A 1 HETATM 9 N NH2 A1ATE . . . L 4 -2.537 6.807 -6.923 1 77.52 ? NH2 A1ATE 511 A 1 HETATM 10 C C01 A1ATE . . . L 4 -1.178 10.716 -7.47 1 80.16 ? C01 A1ATE 511 A 1 HETATM 11 C C03 A1ATE . . . L 4 0.18 11.684 -9.408 1 73.32 ? C03 A1ATE 511 A 1 HETATM 12 C C04 A1ATE . . . L 4 0.425 13.101 -9.905 1 81.51 ? C04 A1ATE 511 A 1 HETATM 13 C C06 A1ATE . . . L 4 -0.796 15.202 -10.401 1 66.57 ? C06 A1ATE 511 A 1 HETATM 14 C C08 A1ATE . . . L 4 -3.356 15.86 -11.264 1 58.23 ? C08 A1ATE 511 A 1 HETATM 15 C C09 A1ATE . . . L 4 -3.083 16.137 -12.759 1 51.76 ? C09 A1ATE 511 A 1 HETATM 16 C C13 A1ATE . . . L 4 -4.258 15.768 -16.466 1 43.33 ? C13 A1ATE 511 A 1 HETATM 17 C C14 A1ATE . . . L 4 -5.637 15.638 -16.445 1 42.42 ? C14 A1ATE 511 A 1 HETATM 18 C C15 A1ATE . . . L 4 -6.308 15.509 -17.631 1 45.3 ? C15 A1ATE 511 A 1 HETATM 19 C C17 A1ATE . . . L 4 -5.607 15.5 -18.823 1 46.11 ? C17 A1ATE 511 A 1 HETATM 20 C C19 A1ATE . . . L 4 -4.238 15.629 -18.842 1 42.98 ? C19 A1ATE 511 A 1 HETATM 21 C C20 A1ATE . . . L 4 -3.558 15.768 -17.653 1 43.55 ? C20 A1ATE 511 A 1 HETATM 22 C C21 A1ATE . . . L 4 -2.638 17.577 -12.937 1 57.96 ? C21 A1ATE 511 A 1 HETATM 23 C C22 A1ATE . . . L 4 -1.443 18.082 -12.193 1 60.92 ? C22 A1ATE 511 A 1 HETATM 24 C C23 A1ATE . . . L 4 -1.486 17.492 -10.751 1 62.45 ? C23 A1ATE 511 A 1 HETATM 25 C C25 A1ATE . . . L 4 -1.88 12.882 -10.622 1 64.71 ? C25 A1ATE 511 A 1 HETATM 26 C C26 A1ATE . . . L 4 -2.242 11.993 -9.445 1 68.83 ? C26 A1ATE 511 A 1 HETATM 27 C C27 A1ATE . . . L 4 -1.278 19.604 -11.878 1 68.19 ? C27 A1ATE 511 A 1 HETATM 28 F F16 A1ATE . . . L 4 -7.654 15.405 -17.611 1 49.77 ? F16 A1ATE 511 A 1 HETATM 29 N N02 A1ATE . . . L 4 -1.091 11.45 -8.742 1 70.47 ? N02 A1ATE 511 A 1 HETATM 30 N N05 A1ATE . . . L 4 -0.788 13.759 -10.316 1 70.05 ? N05 A1ATE 511 A 1 HETATM 31 N N07 A1ATE . . . L 4 -1.918 16.074 -10.764 1 72.39 ? N07 A1ATE 511 A 1 HETATM 32 N N12 A1ATE . . . L 4 -3.508 15.907 -15.247 1 42.54 ? N12 A1ATE 511 A 1 HETATM 33 O O11 A1ATE . . . L 4 -5.285 15.946 -13.725 1 46.36 ? O11 A1ATE 511 A 1 HETATM 34 O O24 A1ATE . . . L 4 0.231 15.699 -10.096 1 80.68 ? O24 A1ATE 511 A 1 HETATM 35 O O27 A1ATE . . . L 4 -0.174 10.32 -6.982 1 85.23 ? O27 A1ATE 511 A 1 HETATM 36 O O28 A1ATE . . . L 4 -0.02 19.724 -11.226 1 77.04 ? O28 A1ATE 511 A 1 HETATM 37 CL CL1 A1ATE . . . L 4 -6.428 15.314 -20.389 1 83.63 ? CL1 A1ATE 511 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 37 #