data_VD1 # _chem_comp.id VD1 _chem_comp.name "5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H36 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "1-ALPHA-HYDROXY-2-METHYLENE-19-NOR-(20S)-BISHOMOPREGNACALCIFEROL; 2MBISP" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-12-17 _chem_comp.pdbx_modified_date 2020-06-17 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 344.531 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VD1 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1RKG _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal VD1 O2 O2 O 0 1 N N N 58.937 8.128 1.083 5.251 -1.514 -0.870 O2 VD1 1 VD1 C3 C3 C 0 1 N N R 60.437 8.098 1.175 5.276 -0.983 0.456 C3 VD1 2 VD1 C2 C2 C 0 1 N N N 60.695 6.869 2.009 5.439 0.519 0.399 C2 VD1 3 VD1 C28 C28 C 0 1 N N N 61.359 7.021 3.137 6.512 1.092 0.884 C28 VD1 4 VD1 C1 C1 C 0 1 N N R 60.264 5.525 1.564 4.341 1.347 -0.228 C1 VD1 5 VD1 O1 O1 O 0 1 N N N 60.781 4.400 2.318 4.641 2.736 -0.075 O1 VD1 6 VD1 C4 C4 C 0 1 N N N 60.939 7.994 -0.229 3.954 -1.306 1.165 C4 VD1 7 VD1 C5 C5 C 0 1 N N N 60.753 6.639 -0.805 2.856 -0.477 0.538 C5 VD1 8 VD1 C10 C10 C 0 1 N N N 60.857 5.418 0.138 3.019 1.025 0.481 C10 VD1 9 VD1 C6 C6 C 0 1 N N N 60.486 6.662 -2.189 1.768 -1.058 0.045 C6 VD1 10 VD1 C7 C7 C 0 1 N N N 60.284 5.418 -2.984 0.651 -0.235 -0.442 C7 VD1 11 VD1 C8 C8 C 0 1 N N N 60.492 5.312 -4.296 -0.478 -0.813 -0.838 C8 VD1 12 VD1 C9 C9 C 0 1 N N N 61.001 6.426 -5.170 -0.674 -2.322 -0.810 C9 VD1 13 VD1 C11 C11 C 0 1 N N N 62.360 5.999 -5.733 -1.983 -2.684 -0.110 C11 VD1 14 VD1 C12 C12 C 0 1 N N N 62.297 4.645 -6.496 -3.163 -1.853 -0.642 C12 VD1 15 VD1 C13 C13 C 0 1 N N R 61.727 3.566 -5.556 -2.836 -0.397 -0.409 C13 VD1 16 VD1 C18 C18 C 0 1 N N N 62.812 3.320 -4.368 -2.408 -0.201 1.047 C18 VD1 17 VD1 C14 C14 C 0 1 N N S 60.288 3.958 -4.964 -1.652 -0.025 -1.339 C14 VD1 18 VD1 C15 C15 C 0 1 N N N 59.665 2.729 -4.352 -1.592 1.492 -1.150 C15 VD1 19 VD1 C17 C17 C 0 1 N N R 61.383 2.179 -6.139 -3.884 0.645 -0.769 C17 VD1 20 VD1 C16 C16 C 0 1 N N N 60.269 1.576 -5.213 -3.093 1.899 -1.166 C16 VD1 21 VD1 C20 C20 C 0 1 N N S 62.497 1.217 -6.581 -4.759 0.960 0.445 C20 VD1 22 VD1 C21 C21 C 0 1 N N N 61.749 0.165 -7.432 -5.805 2.009 0.062 C21 VD1 23 VD1 C22 C22 C 0 1 N N N 63.631 1.891 -7.406 -5.463 -0.316 0.911 C22 VD1 24 VD1 C23 C23 C 0 1 N N N 65.026 1.668 -6.831 -6.240 -0.029 2.198 C23 VD1 25 VD1 HO2 HO2 H 0 1 N N N 58.774 8.902 0.557 6.052 -1.334 -1.381 HO2 VD1 26 VD1 H3 H3 H 0 1 N N N 60.939 8.982 1.632 6.107 -1.420 1.010 H3 VD1 27 VD1 H281 1H28 H 0 0 N N N 61.680 8.022 3.468 7.291 0.491 1.329 H281 VD1 28 VD1 H282 2H28 H 0 0 N N N 61.547 6.121 3.747 6.619 2.166 0.838 H282 VD1 29 VD1 H1 H1 H 0 1 N N N 59.156 5.457 1.671 4.259 1.106 -1.288 H1 VD1 30 VD1 HO1 HO1 H 0 1 N N N 60.504 3.537 2.032 5.472 3.007 -0.488 HO1 VD1 31 VD1 H41 1H4 H 0 1 N N N 60.474 8.772 -0.878 3.725 -2.365 1.048 H41 VD1 32 VD1 H42 2H4 H 0 1 N N N 62.004 8.314 -0.297 4.038 -1.061 2.224 H42 VD1 33 VD1 H101 1H10 H 0 0 N N N 61.926 5.111 0.214 3.038 1.430 1.492 H101 VD1 34 VD1 H102 2H10 H 0 0 N N N 60.413 4.530 -0.371 2.190 1.462 -0.075 H102 VD1 35 VD1 H6 H6 H 0 1 N N N 60.434 7.661 -2.653 1.703 -2.135 0.003 H6 VD1 36 VD1 H7 H7 H 0 1 N N N 59.940 4.463 -2.550 0.748 0.840 -0.479 H7 VD1 37 VD1 H91 1H9 H 0 1 N N N 60.275 6.716 -5.965 -0.697 -2.700 -1.832 H91 VD1 38 VD1 H92 2H9 H 0 1 N N N 61.041 7.406 -4.640 0.157 -2.782 -0.276 H92 VD1 39 VD1 H111 1H11 H 0 0 N N N 62.795 6.799 -6.375 -2.191 -3.741 -0.272 H111 VD1 40 VD1 H112 2H11 H 0 0 N N N 63.133 5.969 -4.930 -1.875 -2.504 0.960 H112 VD1 41 VD1 H121 1H12 H 0 0 N N N 61.725 4.721 -7.450 -3.294 -2.037 -1.708 H121 VD1 42 VD1 H122 2H12 H 0 0 N N N 63.283 4.354 -6.927 -4.074 -2.118 -0.105 H122 VD1 43 VD1 H181 1H18 H 0 0 N N N 62.399 2.539 -3.687 -1.535 -0.819 1.256 H181 VD1 44 VD1 H182 2H18 H 0 0 N N N 63.826 3.065 -4.754 -2.160 0.847 1.215 H182 VD1 45 VD1 H183 3H18 H 0 0 N N N 63.088 4.258 -3.832 -3.225 -0.491 1.708 H183 VD1 46 VD1 H14 H14 H 0 1 N N N 59.425 4.196 -5.628 -1.877 -0.284 -2.373 H14 VD1 47 VD1 H151 1H15 H 0 0 N N N 59.820 2.623 -3.253 -1.134 1.744 -0.193 H151 VD1 48 VD1 H152 2H15 H 0 0 N N N 58.551 2.743 -4.304 -1.055 1.963 -1.973 H152 VD1 49 VD1 H17 H17 H 0 1 N N N 61.019 2.349 -7.179 -4.497 0.294 -1.599 H17 VD1 50 VD1 H161 1H16 H 0 0 N N N 60.640 0.727 -4.592 -3.269 2.710 -0.459 H161 VD1 51 VD1 H162 2H16 H 0 0 N N N 59.492 1.017 -5.785 -3.386 2.208 -2.170 H162 VD1 52 VD1 H20 H20 H 0 1 N N N 63.031 0.795 -5.697 -4.136 1.346 1.252 H20 VD1 53 VD1 H211 1H21 H 0 0 N N N 62.557 -0.533 -7.752 -6.429 2.233 0.927 H211 VD1 54 VD1 H212 2H21 H 0 0 N N N 60.893 -0.326 -6.912 -5.304 2.918 -0.270 H212 VD1 55 VD1 H213 3H21 H 0 0 N N N 61.147 0.590 -8.268 -6.428 1.622 -0.745 H213 VD1 56 VD1 H221 1H22 H 0 0 N N N 63.588 1.565 -8.471 -6.153 -0.653 0.138 H221 VD1 57 VD1 H222 2H22 H 0 0 N N N 63.428 2.979 -7.535 -4.721 -1.092 1.100 H222 VD1 58 VD1 H231 1H23 H 0 0 N N N 65.838 2.151 -7.422 -5.549 0.308 2.971 H231 VD1 59 VD1 H232 2H23 H 0 0 N N N 65.068 1.993 -5.765 -6.981 0.747 2.010 H232 VD1 60 VD1 H233 3H23 H 0 0 N N N 65.228 0.579 -6.701 -6.741 -0.938 2.530 H233 VD1 61 # # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal VD1 O2 C3 SING N N 1 VD1 O2 HO2 SING N N 2 VD1 C3 C2 SING N N 3 VD1 C3 C4 SING N N 4 VD1 C3 H3 SING N N 5 VD1 C2 C28 DOUB N N 6 VD1 C2 C1 SING N N 7 VD1 C28 H281 SING N N 8 VD1 C28 H282 SING N N 9 VD1 C1 O1 SING N N 10 VD1 C1 C10 SING N N 11 VD1 C1 H1 SING N N 12 VD1 O1 HO1 SING N N 13 VD1 C4 C5 SING N N 14 VD1 C4 H41 SING N N 15 VD1 C4 H42 SING N N 16 VD1 C5 C10 SING N N 17 VD1 C5 C6 DOUB N N 18 VD1 C10 H101 SING N N 19 VD1 C10 H102 SING N N 20 VD1 C6 C7 SING N N 21 VD1 C6 H6 SING N N 22 VD1 C7 C8 DOUB N E 23 VD1 C7 H7 SING N N 24 VD1 C8 C9 SING N N 25 VD1 C8 C14 SING N N 26 VD1 C9 C11 SING N N 27 VD1 C9 H91 SING N N 28 VD1 C9 H92 SING N N 29 VD1 C11 C12 SING N N 30 VD1 C11 H111 SING N N 31 VD1 C11 H112 SING N N 32 VD1 C12 C13 SING N N 33 VD1 C12 H121 SING N N 34 VD1 C12 H122 SING N N 35 VD1 C13 C18 SING N N 36 VD1 C13 C14 SING N N 37 VD1 C13 C17 SING N N 38 VD1 C18 H181 SING N N 39 VD1 C18 H182 SING N N 40 VD1 C18 H183 SING N N 41 VD1 C14 C15 SING N N 42 VD1 C14 H14 SING N N 43 VD1 C15 C16 SING N N 44 VD1 C15 H151 SING N N 45 VD1 C15 H152 SING N N 46 VD1 C17 C16 SING N N 47 VD1 C17 C20 SING N N 48 VD1 C17 H17 SING N N 49 VD1 C16 H161 SING N N 50 VD1 C16 H162 SING N N 51 VD1 C20 C21 SING N N 52 VD1 C20 C22 SING N N 53 VD1 C20 H20 SING N N 54 VD1 C21 H211 SING N N 55 VD1 C21 H212 SING N N 56 VD1 C21 H213 SING N N 57 VD1 C22 C23 SING N N 58 VD1 C22 H221 SING N N 59 VD1 C22 H222 SING N N 60 VD1 C23 H231 SING N N 61 VD1 C23 H232 SING N N 62 VD1 C23 H233 SING N N 63 # # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor VD1 SMILES ACDLabs 10.04 "OC3\C(=C)C(O)CC(=C\C=C1/CCCC2(C1CCC2C(C)CC)C)\C3" VD1 InChI InChI 1.03 "InChI=1S/C23H36O2/c1-5-15(2)19-10-11-20-18(7-6-12-23(19,20)4)9-8-17-13-21(24)16(3)22(25)14-17/h8-9,15,19-22,24-25H,3,5-7,10-14H2,1-2,4H3/b18-9+/t15-,19+,20-,21+,22+,23+/m0/s1" VD1 InChIKey InChI 1.03 QSLUXQQUPXBIHH-YHSKWIAJSA-N VD1 SMILES_CANONICAL CACTVS 3.385 "CC[C@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3" VD1 SMILES CACTVS 3.385 "CC[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3" VD1 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "CC[C@H](C)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C" VD1 SMILES "OpenEye OEToolkits" 1.7.5 "CCC(C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C" # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier VD1 "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,3R,7E,17beta)-2-methylidene-17-[(1S)-1-methylpropyl]-9,10-secoestra-5,7-diene-1,3-diol" VD1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2S)-butan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VD1 "Create component" 2003-12-17 EBI VD1 "Modify descriptor" 2011-06-04 RCSB VD1 "Modify descriptor" 2012-01-05 RCSB VD1 "Modify coordinates" 2012-01-05 RCSB VD1 "Modify synonyms" 2020-06-05 PDBE # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 VD1 "1-ALPHA-HYDROXY-2-METHYLENE-19-NOR-(20S)-BISHOMOPREGNACALCIFEROL" ? ? 2 VD1 2MBISP ? ? ##