data_5YCN # _model_server_result.job_id p2B7ESDYMVISFGhaOUUIUQ _model_server_result.datetime_utc '2024-11-14 19:43:56' _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 5ycn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5YCN # _exptl.entry_id 5YCN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 480.536 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5S)-5-[[4-[2-[[6-(4-methoxyphenoxy)pyrimidin-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione _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 5YCN _cell.length_a 130.959 _cell.length_b 53.168 _cell.length_c 54.856 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YCN _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C24 H24 N4 O5 S' _chem_comp.formula_weight 480.536 _chem_comp.id 8LX _chem_comp.mon_nstd_flag . _chem_comp.name (5S)-5-[[4-[2-[[6-(4-methoxyphenoxy)pyrimidin-4-yl]-methyl-amino]ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Lobeglitazone # 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 CBB OBG 8LX sing 1 n n OBG CAY 8LX sing 2 n n CAY CBA 8LX doub 3 n y CAY CAZ 8LX sing 4 n y CBA CAX 8LX sing 5 n y CAZ CAW 8LX doub 6 n y CAX CAV 8LX doub 7 n y CAW CAV 8LX sing 8 n y CAV OBF 8LX sing 9 n n OBF C4 8LX sing 10 n n C4 N3 8LX doub 11 n y C4 C5 8LX sing 12 n y N3 C2 8LX sing 13 n y C5 C6 8LX doub 14 n y C2 N1 8LX doub 15 n y C6 N1 8LX sing 16 n y C6 NAA 8LX sing 17 n n CAR NAA 8LX sing 18 n n NAA CAK 8LX sing 19 n n CAK CAM 8LX sing 20 n n CAM OBC 8LX sing 21 n n OBC CAL 8LX sing 22 n n CAL CAN 8LX doub 23 n y CAL CAO 8LX sing 24 n y CAN CAI 8LX sing 25 n y CAO CAJ 8LX doub 26 n y CAI CAG 8LX doub 27 n y SBH CAE 8LX sing 28 n n SBH CAP 8LX sing 29 n n CAJ CAG 8LX sing 30 n y CAG CAF 8LX sing 31 n n OBE CAP 8LX doub 32 n n CAE CAF 8LX sing 33 n n CAE CAH 8LX sing 34 n n CAP NAB 8LX sing 35 n n NAB CAH 8LX sing 36 n n CAH OBD 8LX doub 37 n n CAE H1 8LX sing 38 n n CAF H2 8LX sing 39 n n CAF H3 8LX sing 40 n n CAI H4 8LX sing 41 n n CAJ H5 8LX sing 42 n n CAK H6 8LX sing 43 n n CAK H7 8LX sing 44 n n CAM H8 8LX sing 45 n n CAM H9 8LX sing 46 n n CAN H10 8LX sing 47 n n CAO H11 8LX sing 48 n n CAR H12 8LX sing 49 n n CAR H13 8LX sing 50 n n CAR H14 8LX sing 51 n n CAW H15 8LX sing 52 n n CAX H16 8LX sing 53 n n CAZ H17 8LX sing 54 n n NAB H18 8LX sing 55 n n CBA H19 8LX sing 56 n n CBB H20 8LX sing 57 n n CBB H21 8LX sing 58 n n CBB H22 8LX sing 59 n n C2 H23 8LX sing 60 n n C5 H24 8LX sing 61 n n # _atom_sites.entry_id 5YCN _atom_sites.fract_transf_matrix[1][1] 0.007636 _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] 0.018808 _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] 0.01823 _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 8LX A 1 501 1 8LX DRG . D 4 HOH A 1 601 53 HOH HOH . D 4 HOH A 2 602 81 HOH HOH . D 4 HOH A 3 603 50 HOH HOH . D 4 HOH A 4 604 29 HOH HOH . D 4 HOH A 5 605 69 HOH HOH . D 4 HOH A 6 606 71 HOH HOH . D 4 HOH A 7 607 101 HOH HOH . D 4 HOH A 8 608 10 HOH HOH . D 4 HOH A 9 609 82 HOH HOH . D 4 HOH A 10 610 65 HOH HOH . D 4 HOH A 11 611 72 HOH HOH . D 4 HOH A 12 612 11 HOH HOH . D 4 HOH A 13 613 103 HOH HOH . D 4 HOH A 14 614 60 HOH HOH . D 4 HOH A 15 615 79 HOH HOH . D 4 HOH A 16 616 5 HOH HOH . D 4 HOH A 17 617 13 HOH HOH . D 4 HOH A 18 618 21 HOH HOH . D 4 HOH A 19 619 57 HOH HOH . D 4 HOH A 20 620 9 HOH HOH . D 4 HOH A 21 621 23 HOH HOH . D 4 HOH A 22 622 14 HOH HOH . D 4 HOH A 23 623 3 HOH HOH . D 4 HOH A 24 624 92 HOH HOH . D 4 HOH A 25 625 88 HOH HOH . D 4 HOH A 26 626 8 HOH HOH . D 4 HOH A 27 627 24 HOH HOH . D 4 HOH A 28 628 67 HOH HOH . D 4 HOH A 29 629 7 HOH HOH . D 4 HOH A 30 630 100 HOH HOH . D 4 HOH A 31 631 39 HOH HOH . D 4 HOH A 32 632 74 HOH HOH . D 4 HOH A 33 633 91 HOH HOH . D 4 HOH A 34 634 73 HOH HOH . D 4 HOH A 35 635 25 HOH HOH . D 4 HOH A 36 636 1 HOH HOH . D 4 HOH A 37 637 33 HOH HOH . D 4 HOH A 38 638 31 HOH HOH . D 4 HOH A 39 639 15 HOH HOH . D 4 HOH A 40 640 6 HOH HOH . D 4 HOH A 41 641 83 HOH HOH . D 4 HOH A 42 642 12 HOH HOH . D 4 HOH A 43 643 77 HOH HOH . D 4 HOH A 44 644 34 HOH HOH . D 4 HOH A 45 645 46 HOH HOH . D 4 HOH A 46 646 89 HOH HOH . D 4 HOH A 47 647 85 HOH HOH . D 4 HOH A 48 648 4 HOH HOH . D 4 HOH A 49 649 54 HOH HOH . D 4 HOH A 50 650 19 HOH HOH . D 4 HOH A 51 651 56 HOH HOH . D 4 HOH A 52 652 94 HOH HOH . D 4 HOH A 53 653 20 HOH HOH . D 4 HOH A 54 654 2 HOH HOH . D 4 HOH A 55 655 70 HOH HOH . D 4 HOH A 56 656 99 HOH HOH . D 4 HOH A 57 657 75 HOH HOH . D 4 HOH A 58 658 16 HOH HOH . D 4 HOH A 59 659 76 HOH HOH . D 4 HOH A 60 660 80 HOH HOH . D 4 HOH A 61 661 58 HOH HOH . D 4 HOH A 62 662 42 HOH HOH . D 4 HOH A 63 663 32 HOH HOH . D 4 HOH A 64 664 37 HOH HOH . D 4 HOH A 65 665 66 HOH HOH . D 4 HOH A 66 666 38 HOH HOH . D 4 HOH A 67 667 17 HOH HOH . D 4 HOH A 68 668 35 HOH HOH . D 4 HOH A 69 669 62 HOH HOH . D 4 HOH A 70 670 36 HOH HOH . D 4 HOH A 71 671 108 HOH HOH . D 4 HOH A 72 672 87 HOH HOH . D 4 HOH A 73 673 28 HOH HOH . D 4 HOH A 74 674 26 HOH HOH . D 4 HOH A 75 675 47 HOH HOH . D 4 HOH A 76 676 22 HOH HOH . D 4 HOH A 77 677 90 HOH HOH . D 4 HOH A 78 678 93 HOH HOH . D 4 HOH A 79 679 55 HOH HOH . D 4 HOH A 80 680 109 HOH HOH . D 4 HOH A 81 681 61 HOH HOH . D 4 HOH A 82 682 98 HOH HOH . D 4 HOH A 83 683 45 HOH HOH . D 4 HOH A 84 684 68 HOH HOH . D 4 HOH A 85 685 84 HOH HOH . D 4 HOH A 86 686 97 HOH HOH . D 4 HOH A 87 687 49 HOH HOH . D 4 HOH A 88 688 52 HOH HOH . D 4 HOH A 89 689 51 HOH HOH . D 4 HOH A 90 690 41 HOH HOH . D 4 HOH A 91 691 48 HOH HOH . D 4 HOH A 92 692 18 HOH HOH . D 4 HOH A 93 693 96 HOH HOH . D 4 HOH A 94 694 106 HOH HOH . D 4 HOH A 95 695 86 HOH HOH . D 4 HOH A 96 696 111 HOH HOH . D 4 HOH A 97 697 40 HOH HOH . D 4 HOH A 98 698 63 HOH HOH . D 4 HOH A 99 699 64 HOH HOH . D 4 HOH A 100 700 27 HOH HOH . D 4 HOH A 101 701 112 HOH HOH . D 4 HOH A 102 702 105 HOH HOH . D 4 HOH A 103 703 43 HOH HOH . D 4 HOH A 104 704 104 HOH HOH . D 4 HOH A 105 705 102 HOH HOH . D 4 HOH A 106 706 44 HOH HOH . D 4 HOH A 107 707 30 HOH HOH . D 4 HOH A 108 708 107 HOH HOH . D 4 HOH A 109 709 95 HOH HOH . D 4 HOH A 110 710 110 HOH HOH . D 4 HOH A 111 711 113 HOH HOH . E 4 HOH B 1 801 59 HOH HOH . E 4 HOH B 2 802 78 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 CAE 8LX . . . C 3 -19.327 7.385 -26.379 1 37.09 ? CAE 8LX 501 A 1 HETATM 2 C CAF 8LX . . . C 3 -18.619 6.369 -25.472 1 33.46 ? CAF 8LX 501 A 1 HETATM 3 C CAG 8LX . . . C 3 -19.515 5.302 -25.253 1 34.14 ? CAG 8LX 501 A 1 HETATM 4 C CAH 8LX . . . C 3 -18.519 8.561 -26.489 1 36.61 ? CAH 8LX 501 A 1 HETATM 5 C CAI 8LX . . . C 3 -19.383 4.116 -25.952 1 35.91 ? CAI 8LX 501 A 1 HETATM 6 C CAJ 8LX . . . C 3 -20.575 5.425 -24.34 1 33.79 ? CAJ 8LX 501 A 1 HETATM 7 C CAK 8LX . . . C 3 -24.216 1.105 -24.096 1 36.48 ? CAK 8LX 501 A 1 HETATM 8 C CAL 8LX . . . C 3 -21.329 3.203 -24.852 1 36.64 ? CAL 8LX 501 A 1 HETATM 9 C CAM 8LX . . . C 3 -23.364 2.368 -24.026 1 36.74 ? CAM 8LX 501 A 1 HETATM 10 C CAN 8LX . . . C 3 -20.291 3.082 -25.749 1 35.49 ? CAN 8LX 501 A 1 HETATM 11 C CAO 8LX . . . C 3 -21.468 4.404 -24.125 1 33.93 ? CAO 8LX 501 A 1 HETATM 12 C CAP 8LX . . . C 3 -18.354 8.054 -28.661 1 38.99 ? CAP 8LX 501 A 1 HETATM 13 C CAR 8LX . . . C 3 -23.978 0.009 -26.411 1 35.32 ? CAR 8LX 501 A 1 HETATM 14 C CAV 8LX . . . C 3 -29.198 2.091 -28.981 1 43.7 ? CAV 8LX 501 A 1 HETATM 15 C CAW 8LX . . . C 3 -29.687 3.087 -29.817 1 46.94 ? CAW 8LX 501 A 1 HETATM 16 C CAX 8LX . . . C 3 -30.057 1.211 -28.333 1 46.26 ? CAX 8LX 501 A 1 HETATM 17 C CAY 8LX . . . C 3 -31.922 2.342 -29.395 1 50.91 ? CAY 8LX 501 A 1 HETATM 18 C CAZ 8LX . . . C 3 -31.047 3.216 -30.047 1 48.11 ? CAZ 8LX 501 A 1 HETATM 19 N NAA 8LX . . . C 3 -24.686 0.936 -25.504 1 35.79 ? NAA 8LX 501 A 1 HETATM 20 N NAB 8LX . . . C 3 -17.951 8.841 -27.68 1 35.52 ? NAB 8LX 501 A 1 HETATM 21 C CBA 8LX . . . C 3 -31.42 1.351 -28.548 1 50.21 ? CBA 8LX 501 A 1 HETATM 22 C CBB 8LX . . . C 3 -33.891 3.701 -29.524 1 59.93 ? CBB 8LX 501 A 1 HETATM 23 O OBC 8LX . . . C 3 -22.159 2.119 -24.739 1 36.39 ? OBC 8LX 501 A 1 HETATM 24 O OBD 8LX . . . C 3 -18.272 9.28 -25.531 1 36.92 ? OBD 8LX 501 A 1 HETATM 25 O OBE 8LX . . . C 3 -17.922 8.144 -29.811 1 40.44 ? OBE 8LX 501 A 1 HETATM 26 O OBF 8LX . . . C 3 -27.861 1.995 -28.842 1 44.53 ? OBF 8LX 501 A 1 HETATM 27 O OBG 8LX . . . C 3 -33.275 2.402 -29.568 1 56.35 ? OBG 8LX 501 A 1 HETATM 28 S SBH 8LX . . . C 3 -19.396 6.85 -28.098 1 37.41 ? SBH 8LX 501 A 1 HETATM 29 N N1 8LX . . . C 3 -26.393 2.457 -25.119 1 36.2 ? N1 8LX 501 A 1 HETATM 30 C C2 8LX . . . C 3 -27.523 3.176 -25.479 1 36.33 ? C2 8LX 501 A 1 HETATM 31 N N3 8LX . . . C 3 -28.018 3.028 -26.767 1 37.32 ? N3 8LX 501 A 1 HETATM 32 C C4 8LX . . . C 3 -27.408 2.166 -27.6 1 39.12 ? C4 8LX 501 A 1 HETATM 33 C C5 8LX . . . C 3 -26.286 1.431 -27.255 1 37.9 ? C5 8LX 501 A 1 HETATM 34 C C6 8LX . . . C 3 -25.768 1.592 -25.961 1 39.03 ? C6 8LX 501 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 645 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #