data_4J5B # _model_server_result.job_id 7WOt7HxkXO0Nl58gyxCcJA _model_server_result.datetime_utc '2024-11-08 12:33:17' _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 4j5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4J5B # _exptl.entry_id 4J5B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.522 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-(4-aminobenzyl)-3-(2-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-2-oxoethyl)urea _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 4J5B _cell.length_a 57.818 _cell.length_b 57.818 _cell.length_c 88.755 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4J5B _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 'C21 H26 N4 O2 S' _chem_comp.formula_weight 398.522 _chem_comp.id 6B4 _chem_comp.mon_nstd_flag . _chem_comp.name 1-(4-aminobenzyl)-3-(2-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-2-oxoethyl)urea _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 CAA SAT 6B4 sing 1 n n SAT CAY 6B4 sing 2 n n CAG CAY 6B4 doub 3 n y CAG CAE 6B4 sing 4 n y CAY CAZ 6B4 sing 5 n y CAE CAF 6B4 doub 6 n y CAZ CBA 6B4 sing 7 n n CAZ CAH 6B4 doub 8 n y CBA CAP 6B4 sing 9 n n CBA N1 6B4 sing 10 n n CAF CAH 6B4 sing 11 n y OAC CAU 6B4 doub 12 n n CAP CAM 6B4 sing 13 n n CA N 6B4 sing 14 n n CA C 6B4 sing 15 n n CAU N 6B4 sing 16 n n CAU N2 6B4 sing 17 n n CAO CAX 6B4 sing 18 n n N1 C 6B4 sing 19 n n N1 CAQ 6B4 sing 20 n n CAM CAQ 6B4 sing 21 n n C O 6B4 doub 22 n n CAX CAL 6B4 doub 23 n y CAX CAK 6B4 sing 24 n y CAL CAJ 6B4 sing 25 n y CAK CAI 6B4 doub 26 n y CAJ CAW 6B4 doub 27 n y CAI CAW 6B4 sing 28 n y CAW N3 6B4 sing 29 n n N2 CAO 6B4 sing 30 n n CAA H1 6B4 sing 31 n n CAA H2 6B4 sing 32 n n CAA H3 6B4 sing 33 n n CAG H4 6B4 sing 34 n n CAE H5 6B4 sing 35 n n CAF H6 6B4 sing 36 n n CAH H7 6B4 sing 37 n n CBA H8 6B4 sing 38 n n CAP H9 6B4 sing 39 n n CAP H10 6B4 sing 40 n n CAM H11 6B4 sing 41 n n CAM H12 6B4 sing 42 n n CAQ H13 6B4 sing 43 n n CAQ H14 6B4 sing 44 n n CA H15 6B4 sing 45 n n CA H16 6B4 sing 46 n n N H17 6B4 sing 47 n n CAO H18 6B4 sing 48 n n CAO H19 6B4 sing 49 n n CAK H20 6B4 sing 50 n n CAI H21 6B4 sing 51 n n CAJ H22 6B4 sing 52 n n CAL H23 6B4 sing 53 n n N2 H24 6B4 sing 54 n n N3 H25 6B4 sing 55 n n N3 H26 6B4 sing 56 n n # _atom_sites.entry_id 4J5B _atom_sites.fract_transf_matrix[1][1] 0.017296 _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] 0.017296 _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] 0.011267 _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 6B4 A 1 301 1 6B4 6B4 . C 3 HOH A 1 401 1 HOH HOH . C 3 HOH A 2 402 2 HOH HOH . C 3 HOH A 3 403 3 HOH HOH . C 3 HOH A 4 404 4 HOH HOH . C 3 HOH A 5 405 5 HOH HOH . C 3 HOH A 6 406 6 HOH HOH . C 3 HOH A 7 407 7 HOH HOH . C 3 HOH A 8 408 8 HOH HOH . C 3 HOH A 9 409 9 HOH HOH . C 3 HOH A 10 410 10 HOH HOH . C 3 HOH A 11 411 11 HOH HOH . C 3 HOH A 12 412 12 HOH HOH . C 3 HOH A 13 413 13 HOH HOH . C 3 HOH A 14 414 14 HOH HOH . C 3 HOH A 15 415 15 HOH HOH . C 3 HOH A 16 416 16 HOH HOH . C 3 HOH A 17 417 17 HOH HOH . C 3 HOH A 18 418 18 HOH HOH . C 3 HOH A 19 419 19 HOH HOH . C 3 HOH A 20 420 20 HOH HOH . C 3 HOH A 21 421 21 HOH HOH . C 3 HOH A 22 422 22 HOH HOH . C 3 HOH A 23 423 23 HOH HOH . C 3 HOH A 24 424 24 HOH HOH . C 3 HOH A 25 425 25 HOH HOH . C 3 HOH A 26 426 26 HOH HOH . C 3 HOH A 27 427 28 HOH HOH . C 3 HOH A 28 428 29 HOH HOH . C 3 HOH A 29 429 30 HOH HOH . C 3 HOH A 30 430 31 HOH HOH . C 3 HOH A 31 431 32 HOH HOH . C 3 HOH A 32 432 33 HOH HOH . C 3 HOH A 33 433 34 HOH HOH . C 3 HOH A 34 434 35 HOH HOH . C 3 HOH A 35 435 36 HOH HOH . C 3 HOH A 36 436 37 HOH HOH . C 3 HOH A 37 437 38 HOH HOH . C 3 HOH A 38 438 39 HOH HOH . C 3 HOH A 39 439 40 HOH HOH . C 3 HOH A 40 440 41 HOH HOH . C 3 HOH A 41 441 42 HOH HOH . C 3 HOH A 42 442 43 HOH HOH . C 3 HOH A 43 443 44 HOH HOH . C 3 HOH A 44 444 45 HOH HOH . C 3 HOH A 45 445 46 HOH HOH . C 3 HOH A 46 446 47 HOH HOH . C 3 HOH A 47 447 48 HOH HOH . C 3 HOH A 48 448 49 HOH HOH . C 3 HOH A 49 449 50 HOH HOH . C 3 HOH A 50 450 52 HOH HOH . C 3 HOH A 51 451 53 HOH HOH . C 3 HOH A 52 452 54 HOH HOH . C 3 HOH A 53 453 55 HOH HOH . C 3 HOH A 54 454 56 HOH HOH . C 3 HOH A 55 455 57 HOH HOH . C 3 HOH A 56 456 58 HOH HOH . C 3 HOH A 57 457 59 HOH HOH . C 3 HOH A 58 458 60 HOH HOH . C 3 HOH A 59 459 61 HOH HOH . C 3 HOH A 60 460 62 HOH HOH . C 3 HOH A 61 461 63 HOH HOH . C 3 HOH A 62 462 64 HOH HOH . C 3 HOH A 63 463 65 HOH HOH . C 3 HOH A 64 464 66 HOH HOH . C 3 HOH A 65 465 67 HOH HOH . C 3 HOH A 66 466 68 HOH HOH . C 3 HOH A 67 467 69 HOH HOH . C 3 HOH A 68 468 70 HOH HOH . C 3 HOH A 69 469 71 HOH HOH . C 3 HOH A 70 470 72 HOH HOH . C 3 HOH A 71 471 74 HOH HOH . C 3 HOH A 72 472 92 HOH HOH . C 3 HOH A 73 473 93 HOH HOH . C 3 HOH A 74 474 94 HOH HOH . C 3 HOH A 75 475 95 HOH HOH . C 3 HOH A 76 476 96 HOH HOH . C 3 HOH A 77 477 97 HOH HOH . C 3 HOH A 78 478 98 HOH HOH . C 3 HOH A 79 479 99 HOH HOH . C 3 HOH A 80 480 100 HOH HOH . C 3 HOH A 81 481 101 HOH HOH . C 3 HOH A 82 482 102 HOH HOH . C 3 HOH A 83 483 103 HOH HOH . C 3 HOH A 84 484 104 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 CAA 6B4 . . . B 2 6.471 22.512 12.968 0.76 50.52 ? CAA 6B4 301 A 1 HETATM 2 S SAT 6B4 . . . B 2 6.882 21.739 14.518 0.76 49 ? SAT 6B4 301 A 1 HETATM 3 C CAY 6B4 . . . B 2 6.581 23.088 15.657 0.76 35.64 ? CAY 6B4 301 A 1 HETATM 4 C CAG 6B4 . . . B 2 6.239 24.342 15.158 0.76 35.84 ? CAG 6B4 301 A 1 HETATM 5 C CAE 6B4 . . . B 2 6.002 25.402 16.017 0.76 35.85 ? CAE 6B4 301 A 1 HETATM 6 C CAF 6B4 . . . B 2 6.122 25.194 17.379 0.76 35.85 ? CAF 6B4 301 A 1 HETATM 7 C CAH 6B4 . . . B 2 6.444 23.935 17.877 0.76 35.63 ? CAH 6B4 301 A 1 HETATM 8 C CAZ 6B4 . . . B 2 6.729 22.857 17.028 0.76 35.39 ? CAZ 6B4 301 A 1 HETATM 9 C CBA 6B4 . . . B 2 7.069 21.496 17.327 0.76 35.13 ? CBA 6B4 301 A 1 HETATM 10 C CAP 6B4 . . . B 2 8.592 21.287 17.777 0.76 33.15 ? CAP 6B4 301 A 1 HETATM 11 C CAM 6B4 . . . B 2 8.604 22.128 18.983 0.76 33.12 ? CAM 6B4 301 A 1 HETATM 12 C CAQ 6B4 . . . B 2 7.515 21.197 19.538 0.76 31.95 ? CAQ 6B4 301 A 1 HETATM 13 N N1 6B4 . . . B 2 6.408 21.235 18.625 0.76 34.73 ? N1 6B4 301 A 1 HETATM 14 C C 6B4 . . . B 2 5.149 20.965 18.998 0.76 34.38 ? C 6B4 301 A 1 HETATM 15 O O 6B4 . . . B 2 4.837 20.665 20.148 0.76 31.56 ? O 6B4 301 A 1 HETATM 16 C CA 6B4 . . . B 2 4.114 20.906 17.883 0.76 34.24 ? CA 6B4 301 A 1 HETATM 17 N N 6B4 . . . B 2 2.936 20.185 18.378 0.76 31.43 ? N 6B4 301 A 1 HETATM 18 C CAU 6B4 . . . B 2 2.76 18.872 18.196 0.76 31.32 ? CAU 6B4 301 A 1 HETATM 19 O OAC 6B4 . . . B 2 3.558 18.176 17.562 0.76 31.41 ? OAC 6B4 301 A 1 HETATM 20 N N2 6B4 . . . B 2 1.64 18.358 18.704 0.76 36.1 ? N2 6B4 301 A 1 HETATM 21 C CAO 6B4 . . . B 2 1.28 16.939 18.599 0.76 36.04 ? CAO 6B4 301 A 1 HETATM 22 C CAX 6B4 . . . B 2 1.059 16.503 19.899 0.76 35.99 ? CAX 6B4 301 A 1 HETATM 23 C CAK 6B4 . . . B 2 2.018 16.777 20.868 0.76 30.9 ? CAK 6B4 301 A 1 HETATM 24 C CAI 6B4 . . . B 2 1.823 16.37 22.179 0.76 32.7 ? CAI 6B4 301 A 1 HETATM 25 C CAW 6B4 . . . B 2 0.663 15.69 22.524 0.76 30.55 ? CAW 6B4 301 A 1 HETATM 26 N N3 6B4 . . . B 2 0.49 15.308 23.787 0.76 30.42 ? N3 6B4 301 A 1 HETATM 27 C CAJ 6B4 . . . B 2 -0.302 15.412 21.556 0.76 30.49 ? CAJ 6B4 301 A 1 HETATM 28 C CAL 6B4 . . . B 2 -0.105 15.823 20.241 0.76 35.7 ? CAL 6B4 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #