data_9BXB # _model_server_result.job_id KwLn_ZP9LsyM5dAcaQrt8w _model_server_result.datetime_utc '2025-07-19 20:33:45' _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 9bxb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":512}' # _entry.id 9BXB # _exptl.entry_id 9BXB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 355.795 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S)-1-(N-carbamimidoylglycyl)-N-(4-chloro-3-fluorophenyl)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 9BXB _cell.length_a 55.836 _cell.length_b 65.373 _cell.length_c 84.045 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BXB _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 _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 M _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 A ND2 ASN 204 A ASN 334 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 A ND2 ASN 225 A ASN 355 1_555 K C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale9 A ND2 ASN 255 A ASN 386 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 A ND2 ASN 311 A ASN 448 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? # _chem_comp.formula 'C15 H19 Cl F N5 O2' _chem_comp.formula_weight 355.795 _chem_comp.id A1AS5 _chem_comp.mon_nstd_flag . _chem_comp.name (3S)-1-(N-carbamimidoylglycyl)-N-(4-chloro-3-fluorophenyl)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 A1AS5 sing 1 n n C19 C17 A1AS5 doub 2 n y C19 C20 A1AS5 sing 3 n y C17 C15 A1AS5 sing 4 n y C20 C13 A1AS5 doub 5 n y C15 F16 A1AS5 sing 6 n n C15 C14 A1AS5 doub 7 n y C13 C14 A1AS5 sing 8 n y C13 N12 A1AS5 sing 9 n n N12 C10 A1AS5 sing 10 n n C10 O11 A1AS5 doub 11 n n C10 C09 A1AS5 sing 12 n n C09 C21 A1AS5 sing 13 n n C09 C08 A1AS5 sing 14 n n C21 C22 A1AS5 sing 15 n n C08 N07 A1AS5 sing 16 n n C22 C23 A1AS5 sing 17 n n N07 C23 A1AS5 sing 18 n n N07 C06 A1AS5 sing 19 n n CD C06 A1AS5 sing 20 n n CD NE A1AS5 sing 21 n n C06 O24 A1AS5 doub 22 n n NE CZ A1AS5 sing 23 n n NH2 CZ A1AS5 doub 24 n n CZ NH1 A1AS5 sing 25 n n CD H1 A1AS5 sing 26 n n CD H2 A1AS5 sing 27 n n NE H3 A1AS5 sing 28 n n NH1 H4 A1AS5 sing 29 n n NH1 H5 A1AS5 sing 30 n n NH2 H6 A1AS5 sing 31 n n C08 H7 A1AS5 sing 32 n n C08 H8 A1AS5 sing 33 n n C09 H9 A1AS5 sing 34 n n C14 H10 A1AS5 sing 35 n n C19 H11 A1AS5 sing 36 n n C20 H12 A1AS5 sing 37 n n C21 H13 A1AS5 sing 38 n n C21 H14 A1AS5 sing 39 n n C22 H15 A1AS5 sing 40 n n C22 H16 A1AS5 sing 41 n n C23 H17 A1AS5 sing 42 n n C23 H18 A1AS5 sing 43 n n N12 H19 A1AS5 sing 44 n n # _atom_sites.entry_id 9BXB _atom_sites.fract_transf_matrix[1][1] 0.01791 _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] 0.015297 _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] 0.011898 _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 2 NAG A 1 510 511 NAG NAG . L 3 EPE A 1 511 512 EPE EPE . M 4 A1AS5 A 1 512 1 A1AS5 MW5 . N 5 HOH A 1 601 2 HOH HOH . N 5 HOH A 2 602 12 HOH HOH . N 5 HOH A 3 603 4 HOH HOH . N 5 HOH A 4 604 27 HOH HOH . N 5 HOH A 5 605 8 HOH HOH . N 5 HOH A 6 606 24 HOH HOH . N 5 HOH A 7 607 17 HOH HOH . N 5 HOH A 8 608 7 HOH HOH . N 5 HOH A 9 609 22 HOH HOH . N 5 HOH A 10 610 9 HOH HOH . N 5 HOH A 11 611 14 HOH HOH . N 5 HOH A 12 612 11 HOH HOH . N 5 HOH A 13 613 16 HOH HOH . N 5 HOH A 14 614 26 HOH HOH . N 5 HOH A 15 615 1 HOH HOH . N 5 HOH A 16 616 28 HOH HOH . N 5 HOH A 17 617 13 HOH HOH . N 5 HOH A 18 618 15 HOH HOH . N 5 HOH A 19 619 20 HOH HOH . N 5 HOH A 20 620 10 HOH HOH . N 5 HOH A 21 621 5 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 A1AS5 . . . M 4 -2.438 16.709 -12.651 1 42.51 ? C10 A1AS5 512 A 1 HETATM 2 C CD A1AS5 . . . M 4 0.415 13.851 -8.623 1 50.93 ? CD A1AS5 512 A 1 HETATM 3 N NE A1AS5 . . . M 4 0.423 13.139 -7.314 1 56.62 ? NE A1AS5 512 A 1 HETATM 4 C CZ A1AS5 . . . M 4 1.442 13.512 -6.348 1 52.63 ? CZ A1AS5 512 A 1 HETATM 5 N NH1 A1AS5 . . . M 4 1.439 12.95 -5.246 1 51.99 ? NH1 A1AS5 512 A 1 HETATM 6 N NH2 A1AS5 . . . M 4 2.302 14.368 -6.602 1 53.74 ? NH2 A1AS5 512 A 1 HETATM 7 C C06 A1AS5 . . . M 4 -0.117 15.302 -8.352 1 49.18 ? C06 A1AS5 512 A 1 HETATM 8 C C08 A1AS5 . . . M 4 -1.51 15.521 -10.666 1 49.08 ? C08 A1AS5 512 A 1 HETATM 9 C C09 A1AS5 . . . M 4 -1.12 16.616 -11.772 1 47.57 ? C09 A1AS5 512 A 1 HETATM 10 C C13 A1AS5 . . . M 4 -3.161 16.709 -15.156 1 39.71 ? C13 A1AS5 512 A 1 HETATM 11 C C14 A1AS5 . . . M 4 -4.478 16.589 -14.974 1 40.52 ? C14 A1AS5 512 A 1 HETATM 12 C C15 A1AS5 . . . M 4 -5.337 16.513 -16.129 1 39.08 ? C15 A1AS5 512 A 1 HETATM 13 C C17 A1AS5 . . . M 4 -4.812 16.509 -17.396 1 37.83 ? C17 A1AS5 512 A 1 HETATM 14 C C19 A1AS5 . . . M 4 -3.487 16.582 -17.57 1 38.31 ? C19 A1AS5 512 A 1 HETATM 15 C C20 A1AS5 . . . M 4 -2.643 16.656 -16.445 1 41.83 ? C20 A1AS5 512 A 1 HETATM 16 C C21 A1AS5 . . . M 4 -0.309 17.695 -11.203 1 48.77 ? C21 A1AS5 512 A 1 HETATM 17 C C22 A1AS5 . . . M 4 -0.255 17.918 -9.764 1 48.09 ? C22 A1AS5 512 A 1 HETATM 18 C C23 A1AS5 . . . M 4 -1.531 17.371 -9.155 1 48.72 ? C23 A1AS5 512 A 1 HETATM 19 F F16 A1AS5 . . . M 4 -6.726 16.445 -16.001 1 36.64 ? F16 A1AS5 512 A 1 HETATM 20 N N07 A1AS5 . . . M 4 -1.057 15.984 -9.322 1 47.79 ? N07 A1AS5 512 A 1 HETATM 21 N N12 A1AS5 . . . M 4 -2.175 16.749 -14.088 1 41.64 ? N12 A1AS5 512 A 1 HETATM 22 O O11 A1AS5 . . . M 4 -3.585 16.604 -12.192 1 40.6 ? O11 A1AS5 512 A 1 HETATM 23 O O24 A1AS5 . . . M 4 0.226 15.908 -7.292 1 49.68 ? O24 A1AS5 512 A 1 HETATM 24 CL CL1 A1AS5 . . . M 4 -5.86 16.409 -18.773 1 54.08 ? CL1 A1AS5 512 A 1 # _model_server_stats.io_time_ms 112 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 224 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #