data_9BXW # _model_server_result.job_id 0dF1IcotQE-HlKoyMrauZQ _model_server_result.datetime_utc '2025-07-19 12:05:32' _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 9bxw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":511}' # _entry.id 9BXW # _exptl.entry_id 9BXW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.967 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,5R)-1-[4-(2-carbamimidamidoethyl)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 9BXW _cell.length_a 62.701 _cell.length_b 66.827 _cell.length_c 92.457 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BXW _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,N,O _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? # _chem_comp.formula 'C21 H31 Cl F N7 O3' _chem_comp.formula_weight 483.967 _chem_comp.id A1ATD _chem_comp.mon_nstd_flag . _chem_comp.name (3S,5R)-1-[4-(2-carbamimidamidoethyl)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 A1ATD sing 1 n n C19 C17 A1ATD doub 2 n y C19 C20 A1ATD sing 3 n y C17 C15 A1ATD sing 4 n y C20 C13 A1ATD doub 5 n y C15 F16 A1ATD sing 6 n n C15 C14 A1ATD doub 7 n y C13 C14 A1ATD sing 8 n y C13 N12 A1ATD sing 9 n n N12 C10 A1ATD sing 10 n n C10 O11 A1ATD doub 11 n n C10 C09 A1ATD sing 12 n n C21 C09 A1ATD sing 13 n n C21 C22 A1ATD sing 14 n n C09 C08 A1ATD sing 15 n n C22 C27 A1ATD sing 16 n n C22 C23 A1ATD sing 17 n n C27 O28 A1ATD sing 18 n n C08 N07 A1ATD sing 19 n n C23 N07 A1ATD sing 20 n n N07 C06 A1ATD sing 21 n n C25 C26 A1ATD sing 22 n n C25 N05 A1ATD sing 23 n n C26 N02 A1ATD sing 24 n n C06 N05 A1ATD sing 25 n n C06 O24 A1ATD doub 26 n n N05 C04 A1ATD sing 27 n n C04 C03 A1ATD sing 28 n n N02 C03 A1ATD sing 29 n n N02 C01 A1ATD sing 30 n n C01 CD A1ATD sing 31 n n CD NE A1ATD sing 32 n n NH2 CZ A1ATD doub 33 n n NE CZ A1ATD sing 34 n n CZ NH1 A1ATD sing 35 n n CD H1 A1ATD sing 36 n n CD H2 A1ATD sing 37 n n NE H3 A1ATD sing 38 n n NH1 H4 A1ATD sing 39 n n NH1 H5 A1ATD sing 40 n n NH2 H6 A1ATD sing 41 n n C01 H7 A1ATD sing 42 n n C01 H8 A1ATD sing 43 n n C03 H9 A1ATD sing 44 n n C03 H10 A1ATD sing 45 n n C04 H11 A1ATD sing 46 n n C04 H12 A1ATD sing 47 n n C08 H13 A1ATD sing 48 n n C08 H14 A1ATD sing 49 n n C09 H15 A1ATD sing 50 n n C14 H16 A1ATD sing 51 n n C19 H17 A1ATD sing 52 n n C20 H18 A1ATD sing 53 n n C21 H19 A1ATD sing 54 n n C21 H20 A1ATD sing 55 n n C22 H21 A1ATD sing 56 n n C23 H22 A1ATD sing 57 n n C23 H23 A1ATD sing 58 n n C25 H24 A1ATD sing 59 n n C25 H25 A1ATD sing 60 n n C26 H26 A1ATD sing 61 n n C26 H27 A1ATD sing 62 n n C27 H28 A1ATD sing 63 n n C27 H29 A1ATD sing 64 n n N12 H31 A1ATD sing 65 n n O28 H32 A1ATD sing 66 n n # _atom_sites.entry_id 9BXW _atom_sites.fract_transf_matrix[1][1] 0.015949 _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] 0.014964 _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] 0.010816 _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 A1ATD A 1 511 1 A1ATD MW5 . M 5 MPD A 1 512 1 MPD MPD . N 5 MPD A 1 513 2 MPD MPD . O 6 HOH A 1 601 40 HOH HOH . O 6 HOH A 2 602 66 HOH HOH . O 6 HOH A 3 603 16 HOH HOH . O 6 HOH A 4 604 42 HOH HOH . O 6 HOH A 5 605 23 HOH HOH . O 6 HOH A 6 606 30 HOH HOH . O 6 HOH A 7 607 80 HOH HOH . O 6 HOH A 8 608 52 HOH HOH . O 6 HOH A 9 609 71 HOH HOH . O 6 HOH A 10 610 29 HOH HOH . O 6 HOH A 11 611 3 HOH HOH . O 6 HOH A 12 612 49 HOH HOH . O 6 HOH A 13 613 43 HOH HOH . O 6 HOH A 14 614 14 HOH HOH . O 6 HOH A 15 615 37 HOH HOH . O 6 HOH A 16 616 22 HOH HOH . O 6 HOH A 17 617 44 HOH HOH . O 6 HOH A 18 618 84 HOH HOH . O 6 HOH A 19 619 55 HOH HOH . O 6 HOH A 20 620 13 HOH HOH . O 6 HOH A 21 621 46 HOH HOH . O 6 HOH A 22 622 79 HOH HOH . O 6 HOH A 23 623 33 HOH HOH . O 6 HOH A 24 624 4 HOH HOH . O 6 HOH A 25 625 57 HOH HOH . O 6 HOH A 26 626 41 HOH HOH . O 6 HOH A 27 627 50 HOH HOH . O 6 HOH A 28 628 24 HOH HOH . O 6 HOH A 29 629 28 HOH HOH . O 6 HOH A 30 630 34 HOH HOH . O 6 HOH A 31 631 9 HOH HOH . O 6 HOH A 32 632 11 HOH HOH . O 6 HOH A 33 633 12 HOH HOH . O 6 HOH A 34 634 69 HOH HOH . O 6 HOH A 35 635 45 HOH HOH . O 6 HOH A 36 636 6 HOH HOH . O 6 HOH A 37 637 59 HOH HOH . O 6 HOH A 38 638 1 HOH HOH . O 6 HOH A 39 639 60 HOH HOH . O 6 HOH A 40 640 68 HOH HOH . O 6 HOH A 41 641 2 HOH HOH . O 6 HOH A 42 642 20 HOH HOH . O 6 HOH A 43 643 19 HOH HOH . O 6 HOH A 44 644 61 HOH HOH . O 6 HOH A 45 645 62 HOH HOH . O 6 HOH A 46 646 65 HOH HOH . O 6 HOH A 47 647 27 HOH HOH . O 6 HOH A 48 648 35 HOH HOH . O 6 HOH A 49 649 78 HOH HOH . O 6 HOH A 50 650 39 HOH HOH . O 6 HOH A 51 651 8 HOH HOH . O 6 HOH A 52 652 51 HOH HOH . O 6 HOH A 53 653 15 HOH HOH . O 6 HOH A 54 654 54 HOH HOH . O 6 HOH A 55 655 32 HOH HOH . O 6 HOH A 56 656 25 HOH HOH . O 6 HOH A 57 657 5 HOH HOH . O 6 HOH A 58 658 7 HOH HOH . O 6 HOH A 59 659 74 HOH HOH . O 6 HOH A 60 660 92 HOH HOH . O 6 HOH A 61 661 26 HOH HOH . O 6 HOH A 62 662 21 HOH HOH . O 6 HOH A 63 663 85 HOH HOH . O 6 HOH A 64 664 38 HOH HOH . O 6 HOH A 65 665 36 HOH HOH . O 6 HOH A 66 666 10 HOH HOH . O 6 HOH A 67 667 17 HOH HOH . O 6 HOH A 68 668 18 HOH HOH . O 6 HOH A 69 669 82 HOH HOH . O 6 HOH A 70 670 76 HOH HOH . O 6 HOH A 71 671 77 HOH HOH . O 6 HOH A 72 672 64 HOH HOH . O 6 HOH A 73 673 31 HOH HOH . O 6 HOH A 74 674 47 HOH HOH . O 6 HOH A 75 675 72 HOH HOH . O 6 HOH A 76 676 58 HOH HOH . O 6 HOH A 77 677 53 HOH HOH . O 6 HOH A 78 678 83 HOH HOH . O 6 HOH A 79 679 73 HOH HOH . O 6 HOH A 80 680 48 HOH HOH . O 6 HOH A 81 681 63 HOH HOH . O 6 HOH A 82 682 70 HOH HOH . O 6 HOH A 83 683 91 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 A1ATD . . . L 4 -3.231 17.424 -15.154 1 44.96 ? C10 A1ATD 511 A 1 HETATM 2 C CD A1ATD . . . L 4 -1.371 11.599 -8.867 1 78.56 ? CD A1ATD 511 A 1 HETATM 3 N NE A1ATD . . . L 4 -1.641 11.421 -7.459 1 81.3 ? NE A1ATD 511 A 1 HETATM 4 C CZ A1ATD . . . L 4 -2.489 10.314 -7.043 1 82.26 ? CZ A1ATD 511 A 1 HETATM 5 N NH1 A1ATD . . . L 4 -2.732 10.14 -5.823 1 82.78 ? NH1 A1ATD 511 A 1 HETATM 6 N NH2 A1ATD . . . L 4 -2.982 9.536 -7.896 1 86.62 ? NH2 A1ATD 511 A 1 HETATM 7 C C01 A1ATD . . . L 4 -0.8 12.975 -9.188 1 79.14 ? C01 A1ATD 511 A 1 HETATM 8 C C03 A1ATD . . . L 4 1.143 13.555 -9.888 1 78.83 ? C03 A1ATD 511 A 1 HETATM 9 C C04 A1ATD . . . L 4 1.276 14.866 -10.654 1 80.66 ? C04 A1ATD 511 A 1 HETATM 10 C C06 A1ATD . . . L 4 0.029 16.904 -11.356 1 66.45 ? C06 A1ATD 511 A 1 HETATM 11 C C08 A1ATD . . . L 4 -2.367 17.259 -12.612 1 55.42 ? C08 A1ATD 511 A 1 HETATM 12 C C09 A1ATD . . . L 4 -2.099 17.595 -14.086 1 48.72 ? C09 A1ATD 511 A 1 HETATM 13 C C13 A1ATD . . . L 4 -3.696 17.326 -17.699 1 44.51 ? C13 A1ATD 511 A 1 HETATM 14 C C14 A1ATD . . . L 4 -5.075 17.255 -17.585 1 42.21 ? C14 A1ATD 511 A 1 HETATM 15 C C15 A1ATD . . . L 4 -5.857 17.087 -18.726 1 46.35 ? C15 A1ATD 511 A 1 HETATM 16 C C17 A1ATD . . . L 4 -5.265 16.969 -19.972 1 47.05 ? C17 A1ATD 511 A 1 HETATM 17 C C19 A1ATD . . . L 4 -3.89 17.018 -20.083 1 47.92 ? C19 A1ATD 511 A 1 HETATM 18 C C20 A1ATD . . . L 4 -3.111 17.187 -18.953 1 49.52 ? C20 A1ATD 511 A 1 HETATM 19 C C21 A1ATD . . . L 4 -1.734 19.038 -14.315 1 49.5 ? C21 A1ATD 511 A 1 HETATM 20 C C22 A1ATD . . . L 4 -0.705 19.648 -13.436 1 55.76 ? C22 A1ATD 511 A 1 HETATM 21 C C23 A1ATD . . . L 4 -0.951 19.173 -11.965 1 60.89 ? C23 A1ATD 511 A 1 HETATM 22 C C25 A1ATD . . . L 4 -0.83 14.514 -11.726 1 62.61 ? C25 A1ATD 511 A 1 HETATM 23 C C26 A1ATD . . . L 4 -0.617 13.039 -11.373 1 78.83 ? C26 A1ATD 511 A 1 HETATM 24 C C27 A1ATD . . . L 4 -0.611 21.203 -13.406 1 58.98 ? C27 A1ATD 511 A 1 HETATM 25 F F16 A1ATD . . . L 4 -7.213 17.034 -18.639 1 41.17 ? F16 A1ATD 511 A 1 HETATM 26 N N02 A1ATD . . . L 4 -0.004 12.817 -10.141 1 78.55 ? N02 A1ATD 511 A 1 HETATM 27 N N05 A1ATD . . . L 4 0.123 15.445 -11.247 1 68.5 ? N05 A1ATD 511 A 1 HETATM 28 N N07 A1ATD . . . L 4 -1.076 17.686 -11.932 1 59.2 ? N07 A1ATD 511 A 1 HETATM 29 N N12 A1ATD . . . L 4 -2.81 17.487 -16.55 1 42.61 ? N12 A1ATD 511 A 1 HETATM 30 O O11 A1ATD . . . L 4 -4.359 17.282 -14.848 1 48.77 ? O11 A1ATD 511 A 1 HETATM 31 O O24 A1ATD . . . L 4 0.929 17.525 -10.905 1 76.22 ? O24 A1ATD 511 A 1 HETATM 32 O O28 A1ATD . . . L 4 0.655 21.473 -12.835 1 60.98 ? O28 A1ATD 511 A 1 HETATM 33 CL CL1 A1ATD . . . L 4 -6.254 16.748 -21.444 1 74.67 ? CL1 A1ATD 511 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 33 #