data_5XI7 # _model_server_result.job_id pfxlCZ8eJzonQb-ZI_Mdww _model_server_result.datetime_utc '2024-11-01 03:37:48' _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 5xi7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":506}' # _entry.id 5XI7 # _exptl.entry_id 5XI7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 372.369 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (6Z)-3-[[2,5-bis(fluoranyl)phenyl]methylidene]-6-[(4-tert-butyl-1H-imidazol-5-yl)methylidene]piperazine-2,5-dione _entity.pdbx_number_of_molecules 2 _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 5XI7 _cell.length_a 105.251 _cell.length_b 157.375 _cell.length_c 182.467 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XI7 _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,P,Q,R,S,T,U,V,W,X,Y,Z,AA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 10 O N N ? 10 U N 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc7 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? metalc ? metalc8 G O3G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc9 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc10 H MG MG . A MG 502 1_555 W O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc11 H MG MG . A MG 502 1_555 W O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc12 H MG MG . A MG 502 1_555 X O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc13 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc14 B OE1 GLU 111 B GLU 111 1_555 M CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc15 J O2A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc16 K MG MG . B MG 502 1_555 X O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc17 K MG MG . B MG 502 1_555 X O HOH . B HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc18 K MG MG . B MG 502 1_555 X O HOH . B HOH 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.993 ? metalc ? metalc19 K MG MG . B MG 502 1_555 Y O HOH . C HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc20 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc21 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc22 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc23 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc24 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc25 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc26 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc27 P O3G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? metalc ? metalc28 P O2B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc29 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc30 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc31 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc32 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc33 S O2G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc34 S O2B GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? # _chem_comp.formula 'C19 H18 F2 N4 O2' _chem_comp.formula_weight 372.369 _chem_comp.id PO7 _chem_comp.mon_nstd_flag . _chem_comp.name (6Z)-3-[[2,5-bis(fluoranyl)phenyl]methylidene]-6-[(4-tert-butyl-1H-imidazol-5-yl)methylidene]piperazine-2,5-dione _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 NAO CAL PO7 doub 431 n y NAO CAV PO7 sing 432 n y CAB CBA PO7 sing 433 n n CAL NAN PO7 sing 434 n y CAV CBA PO7 sing 435 n n CAV CAU PO7 doub 436 n y CBA CAC PO7 sing 437 n n CBA CAA PO7 sing 438 n n NAN CAU PO7 sing 439 n y CAU CAI PO7 sing 440 n n CAI CAZ PO7 doub 441 z n NAQ CAZ PO7 sing 442 n n NAQ CAW PO7 sing 443 n n CAZ CAX PO7 sing 444 n n OAD CAW PO7 doub 445 n n CAW CAY PO7 sing 446 n n CAX OAE PO7 doub 447 n n CAX NAP PO7 sing 448 n n CAY NAP PO7 sing 449 n n CAY CAH PO7 doub 450 z n CAH CAT PO7 sing 451 n n CAT CAM PO7 doub 452 n y CAT CAS PO7 sing 453 n y CAM CAR PO7 sing 454 n y FAG CAS PO7 sing 455 n n CAS CAK PO7 doub 456 n y CAR FAF PO7 sing 457 n n CAR CAJ PO7 doub 458 n y CAK CAJ PO7 sing 459 n y CAK H1 PO7 sing 460 n n CAJ H2 PO7 sing 461 n n CAM H3 PO7 sing 462 n n CAH H4 PO7 sing 463 n n NAQ H6 PO7 sing 464 n n CAI H7 PO7 sing 465 n n NAN H8 PO7 sing 466 n n CAL H9 PO7 sing 467 n n CAB H11 PO7 sing 468 n n CAB H12 PO7 sing 469 n n CAB H13 PO7 sing 470 n n CAC H14 PO7 sing 471 n n CAC H15 PO7 sing 472 n n CAC H16 PO7 sing 473 n n CAA H17 PO7 sing 474 n n CAA H18 PO7 sing 475 n n CAA H19 PO7 sing 476 n n NAP H5 PO7 sing 477 n n # _atom_sites.entry_id 5XI7 _atom_sites.fract_transf_matrix[1][1] 0.009501 _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] 0.006354 _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] 0.00548 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GDP B 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 9 MES B 1 503 505 MES MES . M 7 CA B 1 504 2 CA CA . N 9 MES B 1 505 505 MES MES . O 10 PO7 B 1 506 1 PO7 PO7 . P 5 GTP C 1 501 501 GTP GTP . Q 6 MG C 1 502 502 MG MG . R 7 CA C 1 503 1 CA CA . S 5 GTP D 1 501 501 GTP GTP . T 6 MG D 1 502 502 MG MG . U 10 PO7 D 1 503 2 PO7 PO7 . V 11 ACP F 1 401 401 ACP ACP . W 12 HOH A 1 601 47 HOH HOH . W 12 HOH A 2 602 25 HOH HOH . W 12 HOH A 3 603 48 HOH HOH . W 12 HOH A 4 604 64 HOH HOH . W 12 HOH A 5 605 62 HOH HOH . W 12 HOH A 6 606 49 HOH HOH . W 12 HOH A 7 607 74 HOH HOH . W 12 HOH A 8 608 59 HOH HOH . W 12 HOH A 9 609 22 HOH HOH . W 12 HOH A 10 610 66 HOH HOH . W 12 HOH A 11 611 67 HOH HOH . W 12 HOH A 12 612 99 HOH HOH . W 12 HOH A 13 613 96 HOH HOH . W 12 HOH A 14 614 58 HOH HOH . W 12 HOH A 15 615 68 HOH HOH . W 12 HOH A 16 616 65 HOH HOH . X 12 HOH B 1 601 28 HOH HOH . X 12 HOH B 2 602 50 HOH HOH . X 12 HOH B 3 603 52 HOH HOH . X 12 HOH B 4 604 53 HOH HOH . X 12 HOH B 5 605 54 HOH HOH . X 12 HOH B 6 606 24 HOH HOH . X 12 HOH B 7 607 46 HOH HOH . X 12 HOH B 8 608 45 HOH HOH . X 12 HOH B 9 609 17 HOH HOH . X 12 HOH B 10 610 95 HOH HOH . X 12 HOH B 11 611 27 HOH HOH . X 12 HOH B 12 612 26 HOH HOH . X 12 HOH B 13 613 75 HOH HOH . X 12 HOH B 14 614 56 HOH HOH . X 12 HOH B 15 615 16 HOH HOH . Y 12 HOH C 1 601 43 HOH HOH . Y 12 HOH C 2 602 39 HOH HOH . Y 12 HOH C 3 603 101 HOH HOH . Y 12 HOH C 4 604 90 HOH HOH . Y 12 HOH C 5 605 8 HOH HOH . Y 12 HOH C 6 606 35 HOH HOH . Y 12 HOH C 7 607 37 HOH HOH . Y 12 HOH C 8 608 102 HOH HOH . Y 12 HOH C 9 609 31 HOH HOH . Y 12 HOH C 10 610 13 HOH HOH . Y 12 HOH C 11 611 80 HOH HOH . Y 12 HOH C 12 612 36 HOH HOH . Y 12 HOH C 13 613 79 HOH HOH . Y 12 HOH C 14 614 104 HOH HOH . Y 12 HOH C 15 615 84 HOH HOH . Y 12 HOH C 16 616 15 HOH HOH . Y 12 HOH C 17 617 87 HOH HOH . Y 12 HOH C 18 618 38 HOH HOH . Y 12 HOH C 19 619 40 HOH HOH . Y 12 HOH C 20 620 103 HOH HOH . Y 12 HOH C 21 621 4 HOH HOH . Y 12 HOH C 22 622 30 HOH HOH . Y 12 HOH C 23 623 1 HOH HOH . Y 12 HOH C 24 624 81 HOH HOH . Y 12 HOH C 25 625 6 HOH HOH . Y 12 HOH C 26 626 14 HOH HOH . Y 12 HOH C 27 627 29 HOH HOH . Y 12 HOH C 28 628 93 HOH HOH . Y 12 HOH C 29 629 34 HOH HOH . Y 12 HOH C 30 630 12 HOH HOH . Y 12 HOH C 31 631 82 HOH HOH . Y 12 HOH C 32 632 11 HOH HOH . Y 12 HOH C 33 633 88 HOH HOH . Z 12 HOH E 1 201 3 HOH HOH . Z 12 HOH E 2 202 61 HOH HOH . AA 12 HOH F 1 501 72 HOH HOH . AA 12 HOH F 2 502 70 HOH HOH . AA 12 HOH F 3 503 71 HOH HOH . AA 12 HOH F 4 504 69 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 F FAG PO7 . . . O 10 -18.981 62.705 -32.765 1 60.31 ? FAG PO7 506 B 1 HETATM 2 C CAS PO7 . . . O 10 -18.646 63.979 -32.854 1 55.84 ? CAS PO7 506 B 1 HETATM 3 C CAK PO7 . . . O 10 -18.82 64.73 -31.694 1 54.85 ? CAK PO7 506 B 1 HETATM 4 C CAJ PO7 . . . O 10 -18.493 66.08 -31.707 1 58.13 ? CAJ PO7 506 B 1 HETATM 5 C CAR PO7 . . . O 10 -17.997 66.665 -32.872 1 59.66 ? CAR PO7 506 B 1 HETATM 6 F FAF PO7 . . . O 10 -17.681 67.9 -32.909 1 66.71 ? FAF PO7 506 B 1 HETATM 7 C CAM PO7 . . . O 10 -17.827 65.926 -34.026 1 55.23 ? CAM PO7 506 B 1 HETATM 8 C CAT PO7 . . . O 10 -18.137 64.564 -34.046 1 53.22 ? CAT PO7 506 B 1 HETATM 9 C CAH PO7 . . . O 10 -17.956 63.797 -35.207 1 47.8 ? CAH PO7 506 B 1 HETATM 10 C CAY PO7 . . . O 10 -17.242 64.249 -36.334 1 44.43 ? CAY PO7 506 B 1 HETATM 11 C CAW PO7 . . . O 10 -17.68 63.93 -37.624 1 43.28 ? CAW PO7 506 B 1 HETATM 12 O OAD PO7 . . . O 10 -18.685 63.247 -37.826 1 43.35 ? OAD PO7 506 B 1 HETATM 13 N NAQ PO7 . . . O 10 -16.968 64.4 -38.749 1 41.82 ? NAQ PO7 506 B 1 HETATM 14 N NAP PO7 . . . O 10 -16.061 65.029 -36.221 1 42.74 ? NAP PO7 506 B 1 HETATM 15 C CAX PO7 . . . O 10 -15.356 65.504 -37.345 1 41.01 ? CAX PO7 506 B 1 HETATM 16 O OAE PO7 . . . O 10 -14.346 66.177 -37.134 1 40.7 ? OAE PO7 506 B 1 HETATM 17 C CAZ PO7 . . . O 10 -15.8 65.196 -38.641 1 39.69 ? CAZ PO7 506 B 1 HETATM 18 C CAI PO7 . . . O 10 -15.11 65.646 -39.787 1 37.42 ? CAI PO7 506 B 1 HETATM 19 C CAU PO7 . . . O 10 -15.664 65.637 -41.016 1 36.24 ? CAU PO7 506 B 1 HETATM 20 N NAN PO7 . . . O 10 -16.514 64.695 -41.409 1 36.3 ? NAN PO7 506 B 1 HETATM 21 C CAL PO7 . . . O 10 -16.875 64.949 -42.666 1 36.38 ? CAL PO7 506 B 1 HETATM 22 N NAO PO7 . . . O 10 -16.245 66.047 -43.067 1 35.97 ? NAO PO7 506 B 1 HETATM 23 C CAV PO7 . . . O 10 -15.494 66.485 -42.047 1 35.43 ? CAV PO7 506 B 1 HETATM 24 C CBA PO7 . . . O 10 -14.587 67.748 -42.115 1 34.34 ? CBA PO7 506 B 1 HETATM 25 C CAB PO7 . . . O 10 -14.952 68.622 -43.313 1 33.94 ? CAB PO7 506 B 1 HETATM 26 C CAC PO7 . . . O 10 -13.127 67.309 -42.273 1 34.46 ? CAC PO7 506 B 1 HETATM 27 C CAA PO7 . . . O 10 -14.734 68.613 -40.854 1 34.82 ? CAA PO7 506 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #