data_4JVF # _model_server_result.job_id R2drHDD1bUXKbvOfDuE4qw _model_server_result.datetime_utc '2025-09-07 04:55:57' _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 4jvf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4JVF # _exptl.entry_id 4JVF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 638.8 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate' _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 120 _cell.entry_id 4JVF _cell.length_a 55.91 _cell.length_b 55.91 _cell.length_c 116.67 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JVF _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 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 'C40 H42 N6 O2' _chem_comp.formula_weight 638.8 _chem_comp.id 17X _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate' _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 CAW CAX 17X doub 1 n y CAW CAV 17X sing 2 n y CAX CAE 17X sing 3 n y NAY CAV 17X sing 4 n y NAY CAB 17X doub 5 n y CAV CAC 17X doub 6 n y CAN CAO 17X sing 7 n n CAN NAA 17X sing 8 n n CAE CAF 17X doub 9 n y CAO CAP 17X sing 10 n n CAB NAA 17X sing 11 n n CAB NAD 17X sing 12 n y NAA CAR 17X sing 13 n n CBT CBU 17X sing 14 n n CBT NBV 17X sing 15 n n CAC CAF 17X sing 16 n y CAC NAD 17X sing 17 n y CBU CBQ 17X sing 18 n n CAP CAS 17X sing 19 n n CAP CAQ 17X sing 20 n n NAD CAG 17X sing 21 n n OAU CBP 17X sing 22 n n OAU CAS 17X sing 23 n n CAR CAQ 17X sing 24 n n CBP CBO 17X sing 25 n n NBV CBS 17X sing 26 n n CAS OAT 17X doub 27 n n CBQ CBO 17X sing 28 n n CBQ CBR 17X sing 29 n n CBS CBR 17X sing 30 n n CBO NBH 17X sing 31 n n CAG CAH 17X sing 32 n n CAI CAH 17X doub 33 n y CAI CAJ 17X sing 34 n y CBE CAZ 17X doub 35 n y CBE CBD 17X sing 36 n y CAZ CBA 17X sing 37 n y CAH CAM 17X sing 38 n y CAJ CAK 17X doub 39 n y NBH CBD 17X sing 40 n y NBH CBG 17X sing 41 n y CBD CBC 17X doub 42 n y CBA CBB 17X doub 43 n y CAM CAL 17X doub 44 n y CAK CAL 17X sing 45 n y CBC CBB 17X sing 46 n y CBC NBF 17X sing 47 n y CBG CBI 17X sing 48 n n CBG NBF 17X doub 49 n y CBN CBI 17X doub 50 n y CBN CBM 17X sing 51 n y CBI CBJ 17X sing 52 n y CBM CBL 17X doub 53 n y CBJ CBK 17X doub 54 n y CBL CBK 17X sing 55 n y CAI H1 17X sing 56 n n CAJ H2 17X sing 57 n n CAK H3 17X sing 58 n n CAL H4 17X sing 59 n n CAM H5 17X sing 60 n n CAG H6 17X sing 61 n n CAG H7 17X sing 62 n n CAF H8 17X sing 63 n n CAE H9 17X sing 64 n n CAX H10 17X sing 65 n n CAW H11 17X sing 66 n n CAR H12 17X sing 67 n n CAR H13 17X sing 68 n n CAQ H14 17X sing 69 n n CAQ H15 17X sing 70 n n CAN H16 17X sing 71 n n CAN H17 17X sing 72 n n CAO H18 17X sing 73 n n CAO H19 17X sing 74 n n CAP H20 17X sing 75 n n CBP H21 17X sing 76 n n CBP H22 17X sing 77 n n CBO H23 17X sing 78 n n CBQ H24 17X sing 79 n n CBR H25 17X sing 80 n n CBR H26 17X sing 81 n n CBS H27 17X sing 82 n n CBS H28 17X sing 83 n n NBV H29 17X sing 84 n n CBT H31 17X sing 85 n n CBT H32 17X sing 86 n n CBU H33 17X sing 87 n n CBU H34 17X sing 88 n n CBE H35 17X sing 89 n n CAZ H36 17X sing 90 n n CBA H37 17X sing 91 n n CBB H38 17X sing 92 n n CBJ H39 17X sing 93 n n CBK H40 17X sing 94 n n CBL H41 17X sing 95 n n CBM H42 17X sing 96 n n CBN H43 17X sing 97 n n # _atom_sites.entry_id 4JVF _atom_sites.fract_transf_matrix[1][1] 0.017886 _atom_sites.fract_transf_matrix[1][2] 0.010326 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020653 _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] 0.008571 _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 17X B 1 201 1 17X DRG . C 3 HOH B 1 301 4 HOH HOH . C 3 HOH B 2 302 6 HOH HOH . C 3 HOH B 3 303 7 HOH HOH . C 3 HOH B 4 304 8 HOH HOH . C 3 HOH B 5 305 9 HOH HOH . C 3 HOH B 6 306 11 HOH HOH . C 3 HOH B 7 307 12 HOH HOH . C 3 HOH B 8 308 13 HOH HOH . C 3 HOH B 9 309 14 HOH HOH . C 3 HOH B 10 310 15 HOH HOH . C 3 HOH B 11 311 16 HOH HOH . C 3 HOH B 12 312 17 HOH HOH . C 3 HOH B 13 313 18 HOH HOH . C 3 HOH B 14 314 19 HOH HOH . C 3 HOH B 15 315 20 HOH HOH . C 3 HOH B 16 316 22 HOH HOH . C 3 HOH B 17 317 23 HOH HOH . C 3 HOH B 18 318 24 HOH HOH . C 3 HOH B 19 319 25 HOH HOH . C 3 HOH B 20 320 26 HOH HOH . C 3 HOH B 21 321 27 HOH HOH . C 3 HOH B 22 322 28 HOH HOH . C 3 HOH B 23 323 29 HOH HOH . C 3 HOH B 24 324 30 HOH HOH . C 3 HOH B 25 325 31 HOH HOH . C 3 HOH B 26 326 32 HOH HOH . C 3 HOH B 27 327 34 HOH HOH . C 3 HOH B 28 328 36 HOH HOH . C 3 HOH B 29 329 38 HOH HOH . C 3 HOH B 30 330 39 HOH HOH . C 3 HOH B 31 331 40 HOH HOH . C 3 HOH B 32 332 41 HOH HOH . C 3 HOH B 33 333 43 HOH HOH . C 3 HOH B 34 334 46 HOH HOH . C 3 HOH B 35 335 47 HOH HOH . C 3 HOH B 36 336 49 HOH HOH . C 3 HOH B 37 337 50 HOH HOH . C 3 HOH B 38 338 52 HOH HOH . C 3 HOH B 39 339 53 HOH HOH . C 3 HOH B 40 340 54 HOH HOH . C 3 HOH B 41 341 55 HOH HOH . C 3 HOH B 42 342 57 HOH HOH . C 3 HOH B 43 343 58 HOH HOH . C 3 HOH B 44 344 61 HOH HOH . C 3 HOH B 45 345 62 HOH HOH . C 3 HOH B 46 346 63 HOH HOH . C 3 HOH B 47 347 64 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 CAI 17X . . . B 2 -31.095 10.029 -4.49 1 26.21 ? CAI 17X 201 B 1 HETATM 2 C CAJ 17X . . . B 2 -31.882 10.992 -3.846 1 26.8 ? CAJ 17X 201 B 1 HETATM 3 C CAK 17X . . . B 2 -32.55 10.699 -2.674 1 22.62 ? CAK 17X 201 B 1 HETATM 4 C CAL 17X . . . B 2 -32.421 9.418 -2.18 1 24.95 ? CAL 17X 201 B 1 HETATM 5 C CAM 17X . . . B 2 -31.644 8.458 -2.832 1 24.49 ? CAM 17X 201 B 1 HETATM 6 C CAH 17X . . . B 2 -30.97 8.765 -3.996 1 24.93 ? CAH 17X 201 B 1 HETATM 7 C CAG 17X . . . B 2 -30.189 7.803 -4.633 1 24.05 ? CAG 17X 201 B 1 HETATM 8 N NAD 17X . . . B 2 -30.16 7.939 -6.124 1 25.83 ? NAD 17X 201 B 1 HETATM 9 C CAC 17X . . . B 2 -29.217 8.642 -6.772 1 24.62 ? CAC 17X 201 B 1 HETATM 10 C CAF 17X . . . B 2 -28.21 9.401 -6.322 1 24.46 ? CAF 17X 201 B 1 HETATM 11 C CAE 17X . . . B 2 -27.344 10.071 -7.199 1 25.96 ? CAE 17X 201 B 1 HETATM 12 C CAX 17X . . . B 2 -27.586 9.957 -8.57 1 24.43 ? CAX 17X 201 B 1 HETATM 13 C CAW 17X . . . B 2 -28.686 9.177 -8.987 1 23.72 ? CAW 17X 201 B 1 HETATM 14 C CAV 17X . . . B 2 -29.456 8.547 -8.085 1 24.87 ? CAV 17X 201 B 1 HETATM 15 N NAY 17X . . . B 2 -30.52 7.76 -8.255 1 27.31 ? NAY 17X 201 B 1 HETATM 16 C CAB 17X . . . B 2 -30.939 7.381 -7.065 1 27.99 ? CAB 17X 201 B 1 HETATM 17 N NAA 17X . . . B 2 -32.032 6.603 -6.923 1 31.03 ? NAA 17X 201 B 1 HETATM 18 C CAR 17X . . . B 2 -33.079 6.949 -5.925 1 25.62 ? CAR 17X 201 B 1 HETATM 19 C CAQ 17X . . . B 2 -33.627 5.692 -5.245 1 25.35 ? CAQ 17X 201 B 1 HETATM 20 C CAN 17X . . . B 2 -32.282 5.453 -7.854 1 30.77 ? CAN 17X 201 B 1 HETATM 21 C CAO 17X . . . B 2 -32.863 4.218 -7.131 1 28.51 ? CAO 17X 201 B 1 HETATM 22 C CAP 17X . . . B 2 -34.06 4.569 -6.251 1 25.71 ? CAP 17X 201 B 1 HETATM 23 C CAS 17X . . . B 2 -34.488 3.314 -5.445 1 31.25 ? CAS 17X 201 B 1 HETATM 24 O OAT 17X . . . B 2 -34.047 3.114 -4.317 1 43.92 ? OAT 17X 201 B 1 HETATM 25 O OAU 17X . . . B 2 -35.32 2.392 -6.003 1 36.66 ? OAU 17X 201 B 1 HETATM 26 C CBP 17X . . . B 2 -36.704 2.598 -5.918 1 33.72 ? CBP 17X 201 B 1 HETATM 27 C CBO 17X . . . B 2 -37.45 2.008 -4.732 1 29.4 ? CBO 17X 201 B 1 HETATM 28 C CBQ 17X . . . B 2 -38.866 2.286 -5.238 1 29.07 ? CBQ 17X 201 B 1 HETATM 29 C CBR 17X . . . B 2 -39.911 2.16 -4.161 1 29.18 ? CBR 17X 201 B 1 HETATM 30 C CBS 17X . . . B 2 -41.13 2.84 -4.755 1 27.59 ? CBS 17X 201 B 1 HETATM 31 N NBV 17X . . . B 2 -41.624 2.011 -5.867 1 25.8 ? NBV 17X 201 B 1 HETATM 32 C CBT 17X . . . B 2 -40.635 1.592 -6.891 1 26.42 ? CBT 17X 201 B 1 HETATM 33 C CBU 17X . . . B 2 -39.203 1.41 -6.431 1 25.1 ? CBU 17X 201 B 1 HETATM 34 N NBH 17X . . . B 2 -37.083 2.866 -3.481 1 27.35 ? NBH 17X 201 B 1 HETATM 35 C CBD 17X . . . B 2 -37.011 4.213 -3.476 1 26.52 ? CBD 17X 201 B 1 HETATM 36 C CBE 17X . . . B 2 -37.212 5.11 -4.452 1 25.91 ? CBE 17X 201 B 1 HETATM 37 C CAZ 17X . . . B 2 -37.012 6.474 -4.191 1 26.2 ? CAZ 17X 201 B 1 HETATM 38 C CBA 17X . . . B 2 -36.615 6.914 -2.923 1 22.17 ? CBA 17X 201 B 1 HETATM 39 C CBB 17X . . . B 2 -36.413 5.954 -1.943 1 22.85 ? CBB 17X 201 B 1 HETATM 40 C CBC 17X . . . B 2 -36.618 4.651 -2.247 1 25.11 ? CBC 17X 201 B 1 HETATM 41 N NBF 17X . . . B 2 -36.487 3.599 -1.483 1 22.7 ? NBF 17X 201 B 1 HETATM 42 C CBG 17X . . . B 2 -36.76 2.52 -2.23 1 25.54 ? CBG 17X 201 B 1 HETATM 43 C CBI 17X . . . B 2 -36.725 1.293 -1.671 1 27.01 ? CBI 17X 201 B 1 HETATM 44 C CBJ 17X . . . B 2 -35.607 0.902 -0.873 1 26.54 ? CBJ 17X 201 B 1 HETATM 45 C CBK 17X . . . B 2 -35.608 -0.387 -0.259 1 26.72 ? CBK 17X 201 B 1 HETATM 46 C CBL 17X . . . B 2 -36.702 -1.263 -0.418 1 21.88 ? CBL 17X 201 B 1 HETATM 47 C CBM 17X . . . B 2 -37.807 -0.849 -1.181 1 21.83 ? CBM 17X 201 B 1 HETATM 48 C CBN 17X . . . B 2 -37.83 0.421 -1.784 1 22.46 ? CBN 17X 201 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 363 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #