data_5XPN # _model_server_result.job_id 3RW2WeCZbxjBDmnUwgCSZw _model_server_result.datetime_utc '2025-07-08 03:22:00' _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 5xpn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 5XPN # _exptl.entry_id 5XPN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 494.705 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol _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 95.32 _cell.angle_gamma 90 _cell.entry_id 5XPN _cell.length_a 153.74 _cell.length_b 43.16 _cell.length_c 42.03 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XPN _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _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 # _chem_comp.formula 'C32 H46 O4' _chem_comp.formula_weight 494.705 _chem_comp.id 9RO _chem_comp.mon_nstd_flag . _chem_comp.name (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol _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 C7 C1 9RO doub 86 n n O8 C6 9RO sing 87 n n C1 C6 9RO sing 88 n n C1 C2 9RO sing 89 n n C6 C5 9RO sing 90 n n C2 O9 9RO sing 91 n n C2 C3 9RO sing 92 n n C5 C4 9RO sing 93 n n C3 C4 9RO sing 94 n n C4 C10 9RO doub 95 n n C10 C11 9RO sing 96 n n C11 C12 9RO doub 97 e n C12 C17 9RO sing 98 n n C12 C13 9RO sing 99 n n C18 C17 9RO sing 100 n n C18 C19 9RO sing 101 n n C29 O28 9RO sing 102 n n C23 C16 9RO sing 103 n n C17 C16 9RO sing 104 n n C19 C20 9RO sing 105 n n C13 C14 9RO sing 106 n n C16 C20 9RO sing 107 n n C16 C15 9RO sing 108 n n O28 C27 9RO sing 109 n n C26 C25 9RO sing 110 n n C26 C27 9RO sing 111 n n C14 C15 9RO sing 112 n n C24 C25 9RO sing 113 n n C24 C21 9RO sing 114 n n C20 C21 9RO sing 115 n n C27 C30 9RO sing 116 n n C21 C22 9RO sing 117 n n C30 C31 9RO doub 118 n y C30 C35 9RO sing 119 n y C31 C32 9RO sing 120 n y C35 C34 9RO doub 121 n y C32 C33 9RO doub 122 n y C34 C33 9RO sing 123 n y C33 O36 9RO sing 124 n n O36 H1 9RO sing 125 n n C32 H2 9RO sing 126 n n C31 H3 9RO sing 127 n n C34 H4 9RO sing 128 n n C35 H5 9RO sing 129 n n C27 H6 9RO sing 130 n n C29 H7 9RO sing 131 n n C29 H8 9RO sing 132 n n C29 H9 9RO sing 133 n n C26 H10 9RO sing 134 n n C26 H11 9RO sing 135 n n C25 H12 9RO sing 136 n n C25 H13 9RO sing 137 n n C24 H14 9RO sing 138 n n C24 H15 9RO sing 139 n n C21 H16 9RO sing 140 n n C22 H17 9RO sing 141 n n C22 H18 9RO sing 142 n n C22 H19 9RO sing 143 n n C20 H20 9RO sing 144 n n C23 H21 9RO sing 145 n n C23 H22 9RO sing 146 n n C23 H23 9RO sing 147 n n C15 H24 9RO sing 148 n n C15 H25 9RO sing 149 n n C14 H26 9RO sing 150 n n C14 H27 9RO sing 151 n n C13 H28 9RO sing 152 n n C13 H29 9RO sing 153 n n C19 H30 9RO sing 154 n n C19 H31 9RO sing 155 n n C18 H32 9RO sing 156 n n C18 H33 9RO sing 157 n n C17 H34 9RO sing 158 n n C11 H35 9RO sing 159 n n C10 H36 9RO sing 160 n n C3 H37 9RO sing 161 n n C3 H38 9RO sing 162 n n C2 H39 9RO sing 163 n n O9 H40 9RO sing 164 n n C5 H41 9RO sing 165 n n C5 H42 9RO sing 166 n n C6 H43 9RO sing 167 n n O8 H44 9RO sing 168 n n C7 H45 9RO sing 169 n n C7 H46 9RO sing 170 n n # _atom_sites.entry_id 5XPN _atom_sites.fract_transf_matrix[1][1] 0.006504 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000606 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02317 _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] 0.023895 _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 8BO A 1 501 501 8BO 8BO . D 4 9RO A 1 502 502 9RO 8BO . E 5 HOH A 1 601 601 HOH HOH . E 5 HOH A 2 602 602 HOH HOH . E 5 HOH A 3 603 603 HOH HOH . E 5 HOH A 4 604 604 HOH HOH . E 5 HOH A 5 605 605 HOH HOH . E 5 HOH A 6 606 606 HOH HOH . E 5 HOH A 7 607 607 HOH HOH . E 5 HOH A 8 608 608 HOH HOH . E 5 HOH A 9 609 609 HOH HOH . E 5 HOH A 10 610 610 HOH HOH . E 5 HOH A 11 611 611 HOH HOH . E 5 HOH A 12 612 612 HOH HOH . E 5 HOH A 13 613 613 HOH HOH . E 5 HOH A 14 614 614 HOH HOH . E 5 HOH A 15 615 615 HOH HOH . E 5 HOH A 16 616 616 HOH HOH . E 5 HOH A 17 617 617 HOH HOH . E 5 HOH A 18 618 618 HOH HOH . E 5 HOH A 19 619 619 HOH HOH . E 5 HOH A 20 620 620 HOH HOH . E 5 HOH A 21 621 621 HOH HOH . E 5 HOH A 22 622 622 HOH HOH . E 5 HOH A 23 623 623 HOH HOH . E 5 HOH A 24 624 624 HOH HOH . E 5 HOH A 25 625 625 HOH HOH . E 5 HOH A 26 626 626 HOH HOH . E 5 HOH A 27 627 627 HOH HOH . E 5 HOH A 28 628 628 HOH HOH . E 5 HOH A 29 629 629 HOH HOH . E 5 HOH A 30 630 630 HOH HOH . E 5 HOH A 31 631 631 HOH HOH . E 5 HOH A 32 632 632 HOH HOH . E 5 HOH A 33 633 633 HOH HOH . E 5 HOH A 34 634 634 HOH HOH . E 5 HOH A 35 635 635 HOH HOH . E 5 HOH A 36 636 636 HOH HOH . E 5 HOH A 37 637 637 HOH HOH . E 5 HOH A 38 638 638 HOH HOH . E 5 HOH A 39 639 639 HOH HOH . E 5 HOH A 40 640 640 HOH HOH . E 5 HOH A 41 641 641 HOH HOH . E 5 HOH A 42 642 642 HOH HOH . E 5 HOH A 43 643 643 HOH HOH . E 5 HOH A 44 644 644 HOH HOH . E 5 HOH A 45 645 645 HOH HOH . E 5 HOH A 46 646 646 HOH HOH . E 5 HOH A 47 647 647 HOH HOH . E 5 HOH A 48 648 648 HOH HOH . E 5 HOH A 49 649 649 HOH HOH . E 5 HOH A 50 650 650 HOH HOH . E 5 HOH A 51 651 651 HOH HOH . E 5 HOH A 52 652 652 HOH HOH . E 5 HOH A 53 653 653 HOH HOH . E 5 HOH A 54 654 654 HOH HOH . E 5 HOH A 55 655 655 HOH HOH . E 5 HOH A 56 656 656 HOH HOH . E 5 HOH A 57 657 657 HOH HOH . E 5 HOH A 58 658 658 HOH HOH . E 5 HOH A 59 659 659 HOH HOH . E 5 HOH A 60 660 660 HOH HOH . E 5 HOH A 61 661 661 HOH HOH . E 5 HOH A 62 662 662 HOH HOH . E 5 HOH A 63 663 663 HOH HOH . E 5 HOH A 64 664 664 HOH HOH . E 5 HOH A 65 665 665 HOH HOH . E 5 HOH A 66 666 666 HOH HOH . E 5 HOH A 67 667 667 HOH HOH . E 5 HOH A 68 668 668 HOH HOH . E 5 HOH A 69 669 669 HOH HOH . E 5 HOH A 70 670 670 HOH HOH . E 5 HOH A 71 671 671 HOH HOH . E 5 HOH A 72 672 672 HOH HOH . E 5 HOH A 73 673 673 HOH HOH . E 5 HOH A 74 674 674 HOH HOH . E 5 HOH A 75 675 675 HOH HOH . E 5 HOH A 76 676 676 HOH HOH . E 5 HOH A 77 677 677 HOH HOH . E 5 HOH A 78 678 678 HOH HOH . E 5 HOH A 79 679 679 HOH HOH . E 5 HOH A 80 680 680 HOH HOH . E 5 HOH A 81 681 681 HOH HOH . E 5 HOH A 82 682 682 HOH HOH . E 5 HOH A 83 683 683 HOH HOH . E 5 HOH A 84 684 684 HOH HOH . E 5 HOH A 85 685 685 HOH HOH . E 5 HOH A 86 686 686 HOH HOH . E 5 HOH A 87 687 687 HOH HOH . E 5 HOH A 88 688 688 HOH HOH . E 5 HOH A 89 689 689 HOH HOH . E 5 HOH A 90 690 690 HOH HOH . E 5 HOH A 91 691 691 HOH HOH . E 5 HOH A 92 692 692 HOH HOH . E 5 HOH A 93 693 693 HOH HOH . E 5 HOH A 94 694 694 HOH HOH . E 5 HOH A 95 695 695 HOH HOH . E 5 HOH A 96 696 696 HOH HOH . E 5 HOH A 97 697 697 HOH HOH . E 5 HOH A 98 698 698 HOH HOH . E 5 HOH A 99 699 699 HOH HOH . E 5 HOH A 100 700 700 HOH HOH . E 5 HOH A 101 701 701 HOH HOH . E 5 HOH A 102 702 702 HOH HOH . E 5 HOH A 103 703 703 HOH HOH . E 5 HOH A 104 704 704 HOH HOH . E 5 HOH A 105 705 705 HOH HOH . E 5 HOH A 106 706 706 HOH HOH . E 5 HOH A 107 707 707 HOH HOH . E 5 HOH A 108 708 708 HOH HOH . E 5 HOH A 109 709 709 HOH HOH . E 5 HOH A 110 710 710 HOH HOH . E 5 HOH A 111 711 711 HOH HOH . E 5 HOH A 112 712 712 HOH HOH . E 5 HOH A 113 713 713 HOH HOH . E 5 HOH A 114 714 714 HOH HOH . E 5 HOH A 115 715 715 HOH HOH . E 5 HOH A 116 716 716 HOH HOH . E 5 HOH A 117 717 717 HOH HOH . E 5 HOH A 118 718 718 HOH HOH . E 5 HOH A 119 719 719 HOH HOH . E 5 HOH A 120 720 720 HOH HOH . E 5 HOH A 121 721 721 HOH HOH . E 5 HOH A 122 722 722 HOH HOH . E 5 HOH A 123 723 723 HOH HOH . E 5 HOH A 124 724 724 HOH HOH . E 5 HOH A 125 725 725 HOH HOH . E 5 HOH A 126 726 726 HOH HOH . E 5 HOH A 127 727 727 HOH HOH . E 5 HOH A 128 728 728 HOH HOH . E 5 HOH A 129 729 729 HOH HOH . E 5 HOH A 130 730 730 HOH HOH . E 5 HOH A 131 731 731 HOH HOH . E 5 HOH A 132 732 732 HOH HOH . E 5 HOH A 133 733 733 HOH HOH . E 5 HOH A 134 734 734 HOH HOH . E 5 HOH A 135 735 735 HOH HOH . E 5 HOH A 136 736 736 HOH HOH . E 5 HOH A 137 737 737 HOH HOH . E 5 HOH A 138 738 738 HOH HOH . E 5 HOH A 139 739 739 HOH HOH . E 5 HOH A 140 740 740 HOH HOH . E 5 HOH A 141 741 741 HOH HOH . E 5 HOH A 142 742 742 HOH HOH . E 5 HOH A 143 743 743 HOH HOH . E 5 HOH A 144 744 744 HOH HOH . E 5 HOH A 145 745 745 HOH HOH . E 5 HOH A 146 746 746 HOH HOH . E 5 HOH A 147 747 747 HOH HOH . E 5 HOH A 148 748 748 HOH HOH . E 5 HOH A 149 749 749 HOH HOH . E 5 HOH A 150 750 750 HOH HOH . E 5 HOH A 151 751 751 HOH HOH . E 5 HOH A 152 752 752 HOH HOH . E 5 HOH A 153 753 753 HOH HOH . F 5 HOH C 1 701 701 HOH HOH . F 5 HOH C 2 702 702 HOH HOH . F 5 HOH C 3 703 703 HOH HOH . F 5 HOH C 4 704 704 HOH HOH . F 5 HOH C 5 705 705 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 O O36 9RO . B . D 4 8.142 -2.177 32.228 0.5 55.3 ? O36 9RO 502 A 1 HETATM 2 C C33 9RO . B . D 4 8.371 -1.631 30.991 0.5 48.28 ? C33 9RO 502 A 1 HETATM 3 C C32 9RO . B . D 4 9.028 -2.344 29.977 0.5 46.05 ? C32 9RO 502 A 1 HETATM 4 C C31 9RO . B . D 4 9.225 -1.746 28.729 0.5 41.83 ? C31 9RO 502 A 1 HETATM 5 C C34 9RO . B . D 4 7.918 -0.339 30.742 0.5 46.99 ? C34 9RO 502 A 1 HETATM 6 C C35 9RO . B . D 4 8.111 0.259 29.502 0.5 41.62 ? C35 9RO 502 A 1 HETATM 7 C C30 9RO . B . D 4 8.772 -0.445 28.506 0.5 40.48 ? C30 9RO 502 A 1 HETATM 8 C C27 9RO . B . D 4 8.963 0.227 27.206 0.5 38.13 ? C27 9RO 502 A 1 HETATM 9 O O28 9RO . B . D 4 7.757 -0.003 26.489 0.5 40.83 ? O28 9RO 502 A 1 HETATM 10 C C29 9RO . B . D 4 7.989 -0.46 25.165 0.5 42.31 ? C29 9RO 502 A 1 HETATM 11 C C26 9RO . B . D 4 10.213 -0.31 26.52 0.5 34.41 ? C26 9RO 502 A 1 HETATM 12 C C25 9RO . B . D 4 11.498 0.26 27.139 0.5 31.64 ? C25 9RO 502 A 1 HETATM 13 C C24 9RO . B . D 4 11.963 1.617 26.599 0.5 30.82 ? C24 9RO 502 A 1 HETATM 14 C C21 9RO . B . D 4 12.898 2.401 27.539 0.5 29.8 ? C21 9RO 502 A 1 HETATM 15 C C22 9RO . B . D 4 13.509 1.607 28.686 0.5 31.53 ? C22 9RO 502 A 1 HETATM 16 C C20 9RO . B . D 4 14.083 3.115 26.886 0.5 28.92 ? C20 9RO 502 A 1 HETATM 17 C C16 9RO . B . D 4 13.742 4.474 26.285 0.5 27.6 ? C16 9RO 502 A 1 HETATM 18 C C23 9RO . B . D 4 12.672 4.343 25.196 0.5 25.59 ? C23 9RO 502 A 1 HETATM 19 C C15 9RO . B . D 4 13.342 5.612 27.235 0.5 27.13 ? C15 9RO 502 A 1 HETATM 20 C C14 9RO . B . D 4 13.434 6.981 26.525 0.5 26.23 ? C14 9RO 502 A 1 HETATM 21 C C13 9RO . B . D 4 14.796 7.228 25.844 0.5 26.54 ? C13 9RO 502 A 1 HETATM 22 C C19 9RO . B . D 4 14.881 2.389 25.793 0.5 28.56 ? C19 9RO 502 A 1 HETATM 23 C C18 9RO . B . D 4 15.69 3.506 25.125 0.5 28.23 ? C18 9RO 502 A 1 HETATM 24 C C17 9RO . B . D 4 15.124 4.785 25.748 0.5 26.74 ? C17 9RO 502 A 1 HETATM 25 C C12 9RO . B . D 4 15.021 6.036 24.934 0.5 25.56 ? C12 9RO 502 A 1 HETATM 26 C C11 9RO . B . D 4 15.096 6.059 23.583 0.5 25.08 ? C11 9RO 502 A 1 HETATM 27 C C10 9RO . B . D 4 14.939 7.28 22.792 0.5 24.1 ? C10 9RO 502 A 1 HETATM 28 C C4 9RO . B . D 4 14.769 7.337 21.447 0.5 24.06 ? C4 9RO 502 A 1 HETATM 29 C C3 9RO . B . D 4 14.555 8.715 20.844 0.5 23.33 ? C3 9RO 502 A 1 HETATM 30 C C2 9RO . B . D 4 15.171 8.844 19.448 0.5 23.84 ? C2 9RO 502 A 1 HETATM 31 O O9 9RO . B . D 4 16.608 8.826 19.471 0.5 23.18 ? O9 9RO 502 A 1 HETATM 32 C C5 9RO . B . D 4 14.727 6.105 20.57 0.5 22.84 ? C5 9RO 502 A 1 HETATM 33 C C6 9RO . B . D 4 15.097 6.327 19.097 0.5 22.64 ? C6 9RO 502 A 1 HETATM 34 O O8 9RO . B . D 4 14.457 5.317 18.325 0.5 22.39 ? O8 9RO 502 A 1 HETATM 35 C C1 9RO . B . D 4 14.698 7.688 18.604 0.5 23 ? C1 9RO 502 A 1 HETATM 36 C C7 9RO . B . D 4 13.983 7.856 17.5 0.5 20.72 ? C7 9RO 502 A 1 # _model_server_stats.io_time_ms 88 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #