data_4PID # _model_server_result.job_id x7nSzZ3jri8Pxp5VDh_tFQ _model_server_result.datetime_utc '2024-12-18 07:00:33' _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 4pid # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 4PID # _exptl.entry_id 4PID _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 240.261 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-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 120 _cell.entry_id 4PID _cell.length_a 112.783 _cell.length_b 112.783 _cell.length_c 50.347 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PID _symmetry.cell_setting . _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 D _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 104 A CYS 104 1_555 B SG CYS 10 B CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? covale ? covale1 A SG CYS 122 A CYS 122 1_555 D C12 2UQ . A 2UQ 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.675 ? # _chem_comp.formula 'C13 H12 N4 O' _chem_comp.formula_weight 240.261 _chem_comp.id 2UQ _chem_comp.mon_nstd_flag . _chem_comp.name N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-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 N5 C6 2UQ doub 1 n y N5 C4 2UQ sing 2 n y C6 C1 2UQ sing 3 n y C18 C17 2UQ doub 4 n y C18 C11 2UQ sing 5 n y C17 C16 2UQ sing 6 n y N9 C10 2UQ sing 7 n n N9 C7 2UQ sing 8 n n C10 C11 2UQ sing 9 n n C11 C14 2UQ doub 10 n y C12 C4 2UQ sing 11 n n C12 N13 2UQ doub 12 n n C16 C15 2UQ doub 13 n y C4 N3 2UQ doub 14 n y C1 C7 2UQ sing 15 n n C1 C2 2UQ doub 16 n y C14 C15 2UQ sing 17 n y C7 O8 2UQ doub 18 n n N3 C2 2UQ sing 19 n y C2 H1 2UQ sing 20 n n C12 H2 2UQ sing 21 n n C14 H3 2UQ sing 22 n n C15 H4 2UQ sing 23 n n C16 H5 2UQ sing 24 n n C17 H6 2UQ sing 25 n n C18 H7 2UQ sing 26 n n C6 H8 2UQ sing 27 n n N9 H9 2UQ sing 28 n n C10 H10 2UQ sing 29 n n C10 H11 2UQ sing 30 n n N13 H12 2UQ sing 31 n n # _atom_sites.entry_id 4PID _atom_sites.fract_transf_matrix[1][1] 0.008867 _atom_sites.fract_transf_matrix[1][2] 0.005119 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010238 _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] 0.019862 _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 C 3 ACT A 1 301 600 ACT ACY . D 4 2UQ A 1 302 1 2UQ LI1 . E 5 HOH A 1 401 128 HOH HOH . E 5 HOH A 2 402 136 HOH HOH . E 5 HOH A 3 403 63 HOH HOH . E 5 HOH A 4 404 31 HOH HOH . E 5 HOH A 5 405 75 HOH HOH . E 5 HOH A 6 406 127 HOH HOH . E 5 HOH A 7 407 18 HOH HOH . E 5 HOH A 8 408 84 HOH HOH . E 5 HOH A 9 409 146 HOH HOH . E 5 HOH A 10 410 120 HOH HOH . E 5 HOH A 11 411 100 HOH HOH . E 5 HOH A 12 412 40 HOH HOH . E 5 HOH A 13 413 51 HOH HOH . E 5 HOH A 14 414 4 HOH HOH . E 5 HOH A 15 415 19 HOH HOH . E 5 HOH A 16 416 109 HOH HOH . E 5 HOH A 17 417 83 HOH HOH . E 5 HOH A 18 418 129 HOH HOH . E 5 HOH A 19 419 132 HOH HOH . E 5 HOH A 20 420 143 HOH HOH . E 5 HOH A 21 421 131 HOH HOH . E 5 HOH A 22 422 5 HOH HOH . E 5 HOH A 23 423 148 HOH HOH . E 5 HOH A 24 424 104 HOH HOH . E 5 HOH A 25 425 142 HOH HOH . E 5 HOH A 26 426 21 HOH HOH . E 5 HOH A 27 427 156 HOH HOH . E 5 HOH A 28 428 114 HOH HOH . E 5 HOH A 29 429 26 HOH HOH . E 5 HOH A 30 430 37 HOH HOH . E 5 HOH A 31 431 29 HOH HOH . E 5 HOH A 32 432 154 HOH HOH . E 5 HOH A 33 433 15 HOH HOH . E 5 HOH A 34 434 66 HOH HOH . E 5 HOH A 35 435 90 HOH HOH . E 5 HOH A 36 436 91 HOH HOH . E 5 HOH A 37 437 2 HOH HOH . E 5 HOH A 38 438 152 HOH HOH . E 5 HOH A 39 439 27 HOH HOH . E 5 HOH A 40 440 102 HOH HOH . E 5 HOH A 41 441 73 HOH HOH . E 5 HOH A 42 442 13 HOH HOH . E 5 HOH A 43 443 54 HOH HOH . E 5 HOH A 44 444 134 HOH HOH . E 5 HOH A 45 445 107 HOH HOH . E 5 HOH A 46 446 67 HOH HOH . E 5 HOH A 47 447 87 HOH HOH . E 5 HOH A 48 448 133 HOH HOH . E 5 HOH A 49 449 57 HOH HOH . E 5 HOH A 50 450 65 HOH HOH . E 5 HOH A 51 451 3 HOH HOH . E 5 HOH A 52 452 6 HOH HOH . E 5 HOH A 53 453 7 HOH HOH . E 5 HOH A 54 454 8 HOH HOH . E 5 HOH A 55 455 9 HOH HOH . E 5 HOH A 56 456 10 HOH HOH . E 5 HOH A 57 457 11 HOH HOH . E 5 HOH A 58 458 12 HOH HOH . E 5 HOH A 59 459 14 HOH HOH . E 5 HOH A 60 460 16 HOH HOH . E 5 HOH A 61 461 17 HOH HOH . E 5 HOH A 62 462 23 HOH HOH . E 5 HOH A 63 463 25 HOH HOH . E 5 HOH A 64 464 28 HOH HOH . E 5 HOH A 65 465 30 HOH HOH . E 5 HOH A 66 466 32 HOH HOH . E 5 HOH A 67 467 33 HOH HOH . E 5 HOH A 68 468 34 HOH HOH . E 5 HOH A 69 469 35 HOH HOH . E 5 HOH A 70 470 36 HOH HOH . E 5 HOH A 71 471 38 HOH HOH . E 5 HOH A 72 472 39 HOH HOH . E 5 HOH A 73 473 41 HOH HOH . E 5 HOH A 74 474 42 HOH HOH . E 5 HOH A 75 475 43 HOH HOH . E 5 HOH A 76 476 44 HOH HOH . E 5 HOH A 77 477 45 HOH HOH . E 5 HOH A 78 478 46 HOH HOH . E 5 HOH A 79 479 47 HOH HOH . E 5 HOH A 80 480 48 HOH HOH . E 5 HOH A 81 481 49 HOH HOH . E 5 HOH A 82 482 50 HOH HOH . E 5 HOH A 83 483 53 HOH HOH . E 5 HOH A 84 484 55 HOH HOH . E 5 HOH A 85 485 56 HOH HOH . E 5 HOH A 86 486 58 HOH HOH . E 5 HOH A 87 487 59 HOH HOH . E 5 HOH A 88 488 60 HOH HOH . E 5 HOH A 89 489 61 HOH HOH . E 5 HOH A 90 490 62 HOH HOH . E 5 HOH A 91 491 64 HOH HOH . E 5 HOH A 92 492 68 HOH HOH . E 5 HOH A 93 493 69 HOH HOH . E 5 HOH A 94 494 70 HOH HOH . E 5 HOH A 95 495 71 HOH HOH . E 5 HOH A 96 496 72 HOH HOH . E 5 HOH A 97 497 74 HOH HOH . E 5 HOH A 98 498 76 HOH HOH . E 5 HOH A 99 499 77 HOH HOH . E 5 HOH A 100 500 78 HOH HOH . E 5 HOH A 101 501 79 HOH HOH . E 5 HOH A 102 502 80 HOH HOH . E 5 HOH A 103 503 81 HOH HOH . E 5 HOH A 104 504 82 HOH HOH . E 5 HOH A 105 505 85 HOH HOH . E 5 HOH A 106 506 86 HOH HOH . E 5 HOH A 107 507 89 HOH HOH . E 5 HOH A 108 508 92 HOH HOH . E 5 HOH A 109 509 94 HOH HOH . E 5 HOH A 110 510 95 HOH HOH . E 5 HOH A 111 511 96 HOH HOH . E 5 HOH A 112 512 99 HOH HOH . E 5 HOH A 113 513 101 HOH HOH . E 5 HOH A 114 514 103 HOH HOH . E 5 HOH A 115 515 105 HOH HOH . E 5 HOH A 116 516 108 HOH HOH . E 5 HOH A 117 517 110 HOH HOH . E 5 HOH A 118 518 111 HOH HOH . E 5 HOH A 119 519 112 HOH HOH . E 5 HOH A 120 520 113 HOH HOH . E 5 HOH A 121 521 116 HOH HOH . E 5 HOH A 122 522 117 HOH HOH . E 5 HOH A 123 523 118 HOH HOH . E 5 HOH A 124 524 119 HOH HOH . E 5 HOH A 125 525 122 HOH HOH . E 5 HOH A 126 526 124 HOH HOH . E 5 HOH A 127 527 125 HOH HOH . E 5 HOH A 128 528 135 HOH HOH . E 5 HOH A 129 529 137 HOH HOH . E 5 HOH A 130 530 141 HOH HOH . E 5 HOH A 131 531 144 HOH HOH . E 5 HOH A 132 532 145 HOH HOH . E 5 HOH A 133 533 147 HOH HOH . E 5 HOH A 134 534 149 HOH HOH . E 5 HOH A 135 535 150 HOH HOH . E 5 HOH A 136 536 151 HOH HOH . F 5 HOH B 1 401 130 HOH HOH . F 5 HOH B 2 402 115 HOH HOH . F 5 HOH B 3 403 22 HOH HOH . F 5 HOH B 4 404 93 HOH HOH . F 5 HOH B 5 405 1 HOH HOH . F 5 HOH B 6 406 24 HOH HOH . F 5 HOH B 7 407 98 HOH HOH . F 5 HOH B 8 408 153 HOH HOH . F 5 HOH B 9 409 88 HOH HOH . F 5 HOH B 10 410 97 HOH HOH . F 5 HOH B 11 411 121 HOH HOH . F 5 HOH B 12 412 138 HOH HOH . F 5 HOH B 13 413 139 HOH HOH . F 5 HOH B 14 414 140 HOH HOH . F 5 HOH B 15 415 155 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 C1 2UQ . . . D 4 -24.656 50.45 39.012 1 34.46 ? C1 2UQ 302 A 1 HETATM 2 C C2 2UQ . . . D 4 -23.785 50.651 40.11 1 31.32 ? C2 2UQ 302 A 1 HETATM 3 C C11 2UQ . . . D 4 -27.095 46.431 38.393 1 55.37 ? C11 2UQ 302 A 1 HETATM 4 C C12 2UQ . . . D 4 -21.157 52.717 38.604 1 21.31 ? C12 2UQ 302 A 1 HETATM 5 C C14 2UQ . . . D 4 -25.915 46.074 39.123 1 55.23 ? C14 2UQ 302 A 1 HETATM 6 C C15 2UQ . . . D 4 -25.481 44.726 39.223 1 54.77 ? C15 2UQ 302 A 1 HETATM 7 C C16 2UQ . . . D 4 -26.241 43.69 38.611 1 57.54 ? C16 2UQ 302 A 1 HETATM 8 C C17 2UQ . . . D 4 -27.425 44.012 37.876 1 58.08 ? C17 2UQ 302 A 1 HETATM 9 C C18 2UQ . . . D 4 -27.848 45.374 37.769 1 57.53 ? C18 2UQ 302 A 1 HETATM 10 N N3 2UQ . . . D 4 -22.609 51.375 39.973 1 26.23 ? N3 2UQ 302 A 1 HETATM 11 C C4 2UQ . . . D 4 -22.321 51.87 38.708 1 28.57 ? C4 2UQ 302 A 1 HETATM 12 N N5 2UQ . . . D 4 -23.17 51.721 37.619 1 30.83 ? N5 2UQ 302 A 1 HETATM 13 C C6 2UQ . . . D 4 -24.339 51.023 37.737 1 36.99 ? C6 2UQ 302 A 1 HETATM 14 C C7 2UQ . . . D 4 -25.893 49.548 39.265 1 44.23 ? C7 2UQ 302 A 1 HETATM 15 O O8 2UQ . . . D 4 -26.241 49.366 40.47 1 41.85 ? O8 2UQ 302 A 1 HETATM 16 N N9 2UQ . . . D 4 -26.437 48.881 38.172 1 49.14 ? N9 2UQ 302 A 1 HETATM 17 C C10 2UQ . . . D 4 -27.568 47.925 38.269 1 52.54 ? C10 2UQ 302 A 1 HETATM 18 N N13 2UQ . . . D 4 -20.369 52.762 39.582 1 25.81 ? N13 2UQ 302 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 18 #