data_VDY # _chem_comp.id VDY _chem_comp.name "3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H44 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "25-HYDROXYVITAMIN D3" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-05-18 _chem_comp.pdbx_modified_date 2021-03-01 _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 400.637 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VDY _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1J78 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 VDY O1 O1 O 0 1 N N N -28.787 -57.440 45.430 -1.505 1.897 -7.827 O1 VDY 1 VDY O2 O2 O 0 1 N N N -17.338 -54.894 48.355 -2.743 0.908 6.676 O2 VDY 2 VDY C1 C1 C 0 1 N N N -25.736 -55.906 43.634 -2.714 -0.417 -5.126 C1 VDY 3 VDY C2 C2 C 0 1 N N N -27.219 -56.325 43.882 -2.590 0.170 -6.535 C2 VDY 4 VDY C3 C3 C 0 1 N N S -27.394 -57.240 45.115 -1.512 1.254 -6.551 C3 VDY 5 VDY C4 C4 C 0 1 N N N -26.701 -56.653 46.357 -0.140 0.625 -6.290 C4 VDY 6 VDY C5 C5 C 0 1 N N N -25.240 -56.334 46.083 -0.191 -0.096 -4.959 C5 VDY 7 VDY C6 C6 C 0 1 N N N -24.252 -56.928 46.781 0.784 0.047 -4.038 C6 VDY 8 VDY C7 C7 C 0 1 N N N -22.872 -57.049 46.390 0.699 -0.667 -2.763 C7 VDY 9 VDY C8 C8 C 0 1 N N N -21.768 -57.101 47.147 1.663 -0.525 -1.854 C8 VDY 10 VDY C9 C9 C 0 1 N N N -21.731 -57.039 48.663 2.877 0.364 -2.084 C9 VDY 11 VDY C10 C10 C 0 1 N N N -25.063 -55.397 44.895 -1.358 -0.970 -4.720 C10 VDY 12 VDY C11 C11 C 0 1 N N N -20.863 -58.150 49.269 3.089 1.305 -0.900 C11 VDY 13 VDY C12 C12 C 0 1 N N N -19.453 -58.240 48.625 3.039 0.555 0.441 C12 VDY 14 VDY C13 C13 C 0 1 N N R -19.475 -58.373 47.073 1.695 -0.116 0.552 C13 VDY 15 VDY C14 C14 C 0 1 N N S -20.370 -57.188 46.525 1.631 -1.231 -0.531 C14 VDY 16 VDY C15 C15 C 0 1 N N N -20.205 -57.325 44.973 0.323 -1.935 -0.160 C15 VDY 17 VDY C16 C16 C 0 1 N N N -18.761 -57.851 44.798 0.399 -2.004 1.391 C16 VDY 18 VDY C17 C17 C 0 1 N N R -18.187 -57.956 46.221 1.345 -0.857 1.833 C17 VDY 19 VDY C18 C18 C 0 1 N N N -20.060 -59.782 46.690 0.595 0.900 0.242 C18 VDY 20 VDY C19 C19 C 0 1 N N N -24.416 -54.225 44.926 -1.232 -2.177 -4.169 C19 VDY 21 VDY C20 C20 C 0 1 N N R -16.833 -58.765 46.226 0.627 0.077 2.808 C20 VDY 22 VDY C21 C21 C 0 1 N N N -16.880 -60.294 46.023 1.552 1.238 3.176 C21 VDY 23 VDY C22 C22 C 0 1 N N N -16.036 -58.450 47.537 0.252 -0.697 4.074 C22 VDY 24 VDY C23 C23 C 0 1 N N N -15.425 -57.048 47.650 -0.465 0.237 5.049 C23 VDY 25 VDY C24 C24 C 0 1 N N N -15.634 -56.451 49.066 -0.840 -0.536 6.315 C24 VDY 26 VDY C25 C25 C 0 1 N N N -16.197 -55.030 49.240 -1.558 0.398 7.291 C25 VDY 27 VDY C26 C26 C 0 1 N N N -16.685 -54.767 50.658 -1.933 -0.376 8.556 C26 VDY 28 VDY C27 C27 C 0 1 N N N -15.148 -53.977 48.845 -0.633 1.559 7.658 C27 VDY 29 VDY HO1 HO1 H 0 1 N N N -28.895 -58.002 46.188 -0.817 2.576 -7.795 HO1 VDY 30 VDY HO2 HO2 H 0 1 N N N -17.686 -54.016 48.463 -3.297 0.146 6.461 HO2 VDY 31 VDY H11 1H1 H 0 1 N N N -25.661 -55.160 42.809 -3.450 -1.221 -5.128 H11 VDY 32 VDY H12 2H1 H 0 1 N N N -25.154 -56.739 43.175 -3.021 0.361 -4.429 H12 VDY 33 VDY H21 1H2 H 0 1 N N N -27.655 -56.798 42.972 -3.545 0.605 -6.832 H21 VDY 34 VDY H22 2H2 H 0 1 N N N -27.878 -55.428 43.956 -2.320 -0.619 -7.236 H22 VDY 35 VDY H31 1H3 H 0 1 N N N -26.924 -58.215 44.849 -1.727 1.990 -5.776 H31 VDY 36 VDY H41 1H4 H 0 1 N N N -26.813 -57.323 47.241 0.620 1.405 -6.256 H41 VDY 37 VDY H42 2H4 H 0 1 N N N -27.247 -55.762 46.745 0.095 -0.083 -7.084 H42 VDY 38 VDY H61 1H6 H 0 1 N N N -24.598 -57.345 47.742 1.628 0.689 -4.242 H61 VDY 39 VDY H71 1H7 H 0 1 N N N -22.615 -57.113 45.319 -0.144 -1.309 -2.559 H71 VDY 40 VDY H91 1H9 H 0 1 N N N -22.760 -57.052 49.092 3.761 -0.260 -2.209 H91 VDY 41 VDY H92 2H9 H 0 1 N N N -21.404 -56.034 49.017 2.723 0.953 -2.988 H92 VDY 42 VDY H111 1H11 H 0 0 N N N -21.386 -59.134 49.221 4.061 1.789 -1.001 H111 VDY 43 VDY H112 2H11 H 0 0 N N N -20.788 -58.037 50.376 2.311 2.069 -0.910 H112 VDY 44 VDY H121 1H12 H 0 0 N N N -18.866 -59.071 49.081 3.824 -0.199 0.472 H121 VDY 45 VDY H122 2H12 H 0 0 N N N -18.824 -57.373 48.935 3.168 1.259 1.263 H122 VDY 46 VDY H141 1H14 H 0 0 N N N -20.053 -56.166 46.838 2.476 -1.912 -0.437 H141 VDY 47 VDY H151 1H15 H 0 0 N N N -20.426 -56.392 44.404 0.288 -2.936 -0.590 H151 VDY 48 VDY H152 2H15 H 0 0 N N N -20.985 -57.952 44.482 -0.536 -1.346 -0.478 H152 VDY 49 VDY H161 1H16 H 0 0 N N N -18.139 -57.234 44.108 0.806 -2.966 1.703 H161 VDY 50 VDY H162 2H16 H 0 0 N N N -18.697 -58.801 44.218 -0.591 -1.859 1.821 H162 VDY 51 VDY H171 1H17 H 0 0 N N N -17.775 -57.049 46.722 2.245 -1.264 2.293 H171 VDY 52 VDY H181 1H18 H 0 0 N N N -21.061 -59.965 47.147 0.735 1.293 -0.764 H181 VDY 53 VDY H182 2H18 H 0 0 N N N -20.076 -59.877 45.579 -0.378 0.414 0.310 H182 VDY 54 VDY H183 3H18 H 0 0 N N N -19.510 -60.618 47.181 0.643 1.718 0.961 H183 VDY 55 VDY H191 1H19 H 0 0 N N N -23.927 -53.855 45.843 -0.256 -2.544 -3.890 H191 VDY 56 VDY H192 2H19 H 0 0 N N N -24.288 -53.547 44.066 -2.107 -2.789 -4.003 H192 VDY 57 VDY H201 1H20 H 0 0 N N N -16.332 -58.400 45.300 -0.276 0.466 2.340 H201 VDY 58 VDY H211 1H21 H 0 0 N N N -17.428 -60.515 45.078 2.455 0.849 3.645 H211 VDY 59 VDY H212 2H21 H 0 0 N N N -15.923 -60.866 46.027 1.819 1.790 2.275 H212 VDY 60 VDY H213 3H21 H 0 0 N N N -17.567 -60.737 46.781 1.040 1.904 3.871 H213 VDY 61 VDY H221 1H22 H 0 0 N N N -15.241 -59.218 47.685 -0.406 -1.524 3.812 H221 VDY 62 VDY H222 2H22 H 0 0 N N N -16.681 -58.650 48.424 1.156 -1.086 4.542 H222 VDY 63 VDY H231 1H23 H 0 0 N N N -15.816 -56.367 46.858 0.193 1.065 5.312 H231 VDY 64 VDY H232 2H23 H 0 0 N N N -14.348 -57.047 47.362 -1.369 0.627 4.581 H232 VDY 65 VDY H241 1H24 H 0 0 N N N -14.667 -56.513 49.617 -1.499 -1.364 6.053 H241 VDY 66 VDY H242 2H24 H 0 0 N N N -16.273 -57.154 49.650 0.063 -0.926 6.783 H242 VDY 67 VDY H261 1H26 H 0 0 N N N -17.542 -55.417 50.951 -2.444 0.289 9.251 H261 VDY 68 VDY H262 2H26 H 0 0 N N N -15.808 -54.871 51.338 -2.592 -1.203 8.294 H262 VDY 69 VDY H263 3H26 H 0 0 N N N -17.204 -53.786 50.765 -1.029 -0.765 9.025 H263 VDY 70 VDY H271 1H27 H 0 0 N N N -15.562 -52.942 48.836 0.270 1.170 8.127 H271 VDY 71 VDY H272 2H27 H 0 0 N N N -14.271 -54.082 49.525 -0.366 2.111 6.757 H272 VDY 72 VDY H273 3H27 H 0 0 N N N -14.865 -54.037 47.768 -1.145 2.225 8.354 H273 VDY 73 # # 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 VDY O1 C3 SING N N 1 VDY O1 HO1 SING N N 2 VDY O2 C25 SING N N 3 VDY O2 HO2 SING N N 4 VDY C1 C2 SING N N 5 VDY C1 C10 SING N N 6 VDY C1 H11 SING N N 7 VDY C1 H12 SING N N 8 VDY C2 C3 SING N N 9 VDY C2 H21 SING N N 10 VDY C2 H22 SING N N 11 VDY C3 C4 SING N N 12 VDY C3 H31 SING N N 13 VDY C4 C5 SING N N 14 VDY C4 H41 SING N N 15 VDY C4 H42 SING N N 16 VDY C5 C6 DOUB N Z 17 VDY C5 C10 SING N N 18 VDY C6 C7 SING N N 19 VDY C6 H61 SING N N 20 VDY C7 C8 DOUB N E 21 VDY C7 H71 SING N N 22 VDY C8 C9 SING N N 23 VDY C8 C14 SING N N 24 VDY C9 C11 SING N N 25 VDY C9 H91 SING N N 26 VDY C9 H92 SING N N 27 VDY C10 C19 DOUB N N 28 VDY C11 C12 SING N N 29 VDY C11 H111 SING N N 30 VDY C11 H112 SING N N 31 VDY C12 C13 SING N N 32 VDY C12 H121 SING N N 33 VDY C12 H122 SING N N 34 VDY C13 C14 SING N N 35 VDY C13 C17 SING N N 36 VDY C13 C18 SING N N 37 VDY C14 C15 SING N N 38 VDY C14 H141 SING N N 39 VDY C15 C16 SING N N 40 VDY C15 H151 SING N N 41 VDY C15 H152 SING N N 42 VDY C16 C17 SING N N 43 VDY C16 H161 SING N N 44 VDY C16 H162 SING N N 45 VDY C17 C20 SING N N 46 VDY C17 H171 SING N N 47 VDY C18 H181 SING N N 48 VDY C18 H182 SING N N 49 VDY C18 H183 SING N N 50 VDY C19 H191 SING N N 51 VDY C19 H192 SING N N 52 VDY C20 C21 SING N N 53 VDY C20 C22 SING N N 54 VDY C20 H201 SING N N 55 VDY C21 H211 SING N N 56 VDY C21 H212 SING N N 57 VDY C21 H213 SING N N 58 VDY C22 C23 SING N N 59 VDY C22 H221 SING N N 60 VDY C22 H222 SING N N 61 VDY C23 C24 SING N N 62 VDY C23 H231 SING N N 63 VDY C23 H232 SING N N 64 VDY C24 C25 SING N N 65 VDY C24 H241 SING N N 66 VDY C24 H242 SING N N 67 VDY C25 C26 SING N N 68 VDY C25 C27 SING N N 69 VDY C26 H261 SING N N 70 VDY C26 H262 SING N N 71 VDY C26 H263 SING N N 72 VDY C27 H271 SING N N 73 VDY C27 H272 SING N N 74 VDY C27 H273 SING N N 75 # # 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 VDY SMILES ACDLabs 10.04 "OC3CC(=C/C=C1\CCCC2(C)C(C(C)CCCC(O)(C)C)CCC12)/C(=C)CC3" VDY SMILES_CANONICAL CACTVS 3.341 "C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)CCC3=C" VDY SMILES CACTVS 3.341 "C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)CCC3=C" VDY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](CCC3=C)O)C" VDY SMILES "OpenEye OEToolkits" 1.5.0 "CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(CCC3=C)O)C" VDY InChI InChI 1.03 "InChI=1S/C27H44O2/c1-19-10-13-23(28)18-22(19)12-11-21-9-7-17-27(5)24(14-15-25(21)27)20(2)8-6-16-26(3,4)29/h11-12,20,23-25,28-29H,1,6-10,13-18H2,2-5H3/b21-11+,22-12-/t20-,23+,24-,25+,27-/m1/s1" VDY InChIKey InChI 1.03 JWUBBDSIWDLEOM-DTOXIADCSA-N # # 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 VDY "SYSTEMATIC NAME" ACDLabs 10.04 "(3S,5Z,14beta,17alpha)-9,10-secocholesta-5,7,10-triene-3,25-diol" VDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1S)-3-[(2E)-2-[(1R,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VDY "Create component" 2001-05-18 PDBJ VDY "Modify descriptor" 2011-06-04 RCSB VDY "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id VDY _pdbx_chem_comp_synonyms.name "25-HYDROXYVITAMIN D3" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##