data_VDZ # _chem_comp.id VDZ _chem_comp.name ;5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIO L ; _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H44 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-METHYLENE-19-NOR-(20S)-1ALPHA,25-DIHYDROXY-VITAMIN D3; 2MD" _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 416.636 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VDZ _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 1RJK _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 VDZ O1 O1 O 0 1 N N N 60.750 4.465 2.321 -3.583 1.478 1.706 O1 VDZ 1 VDZ C1 C1 C 0 1 N N R 60.342 5.624 1.550 -4.836 0.790 1.675 C1 VDZ 2 VDZ C2 C2 C 0 1 N N N 60.774 6.948 2.031 -5.851 1.619 0.921 C2 VDZ 3 VDZ C28 C28 C 0 1 N N N 61.437 7.054 3.164 -6.907 2.097 1.532 C28 VDZ 4 VDZ C3 C3 C 0 1 N N R 60.568 8.207 1.231 -5.627 1.886 -0.550 C3 VDZ 5 VDZ O2 O2 O 0 1 N N N 59.068 8.230 1.261 -6.753 2.582 -1.088 O2 VDZ 6 VDZ C4 C4 C 0 1 N N N 60.935 8.127 -0.223 -5.458 0.543 -1.271 C4 VDZ 7 VDZ C10 C10 C 0 1 N N N 60.912 5.543 0.105 -4.667 -0.553 0.953 C10 VDZ 8 VDZ C5 C5 C 0 1 N N N 60.738 6.773 -0.822 -4.443 -0.285 -0.517 C5 VDZ 9 VDZ C6 C6 C 0 1 N N N 60.373 6.819 -2.186 -3.372 -0.770 -1.137 C6 VDZ 10 VDZ C7 C7 C 0 1 N N N 60.087 5.589 -2.985 -2.336 -1.478 -0.369 C7 VDZ 11 VDZ C8 C8 C 0 1 N N N 60.417 5.432 -4.250 -1.216 -1.870 -0.968 C8 VDZ 12 VDZ C9 C9 C 0 1 N N N 61.209 6.465 -5.004 -0.949 -1.615 -2.445 C9 VDZ 13 VDZ C11 C11 C 0 1 N N N 62.524 5.788 -5.463 0.426 -0.980 -2.644 C11 VDZ 14 VDZ C14 C14 C 0 1 N N S 60.079 4.108 -4.903 -0.123 -2.590 -0.236 C14 VDZ 15 VDZ C13 C13 C 0 1 N N R 61.472 3.461 -5.335 1.147 -1.710 -0.415 C13 VDZ 16 VDZ C12 C12 C 0 1 N N N 62.385 4.401 -6.141 1.521 -1.739 -1.875 C12 VDZ 17 VDZ C18 C18 C 0 1 N N N 62.288 3.114 -3.984 0.825 -0.273 -0.001 C18 VDZ 18 VDZ C15 C15 C 0 1 N N N 59.198 3.027 -4.321 -0.236 -2.644 1.289 C15 VDZ 19 VDZ C16 C16 C 0 1 N N N 59.651 1.753 -5.105 1.238 -2.854 1.736 C16 VDZ 20 VDZ C17 C17 C 0 1 N N R 60.946 2.140 -5.909 2.124 -2.302 0.589 C17 VDZ 21 VDZ C20 C20 C 0 1 N N S 61.840 0.914 -6.008 3.064 -1.217 1.119 C20 VDZ 22 VDZ C21 C21 C 0 1 N N N 61.004 -0.108 -6.815 4.037 -1.833 2.126 C21 VDZ 23 VDZ C22 C22 C 0 1 N N N 63.271 1.147 -6.557 3.850 -0.610 -0.045 C22 VDZ 24 VDZ C23 C23 C 0 1 N N N 64.070 -0.151 -6.592 4.697 0.557 0.466 C23 VDZ 25 VDZ C24 C24 C 0 1 N N N 65.574 0.014 -6.804 5.484 1.164 -0.698 C24 VDZ 26 VDZ C25 C25 C 0 1 N N N 66.378 -1.318 -6.672 6.331 2.331 -0.188 C25 VDZ 27 VDZ C26 C26 C 0 1 N N N 67.692 -1.049 -7.347 7.305 1.826 0.878 C26 VDZ 28 VDZ C27 C27 C 0 1 N N N 66.537 -1.890 -5.234 7.117 2.938 -1.351 C27 VDZ 29 VDZ O3 O3 O 0 1 N N N 65.723 -2.313 -7.402 5.477 3.326 0.381 O3 VDZ 30 VDZ HO1 HO1 H 0 1 N N N 60.471 3.611 2.010 -3.621 2.343 2.137 HO1 VDZ 31 VDZ H1 H1 H 0 1 N N N 59.231 5.567 1.633 -5.185 0.621 2.693 H1 VDZ 32 VDZ H281 1H28 H 0 0 N N N 61.587 6.131 3.750 -7.058 1.900 2.583 H281 VDZ 33 VDZ H282 2H28 H 0 0 N N N 61.760 8.045 3.524 -7.626 2.687 0.984 H282 VDZ 34 VDZ H3 H3 H 0 1 N N N 61.168 9.055 1.635 -4.728 2.489 -0.679 H3 VDZ 35 VDZ HO2 HO2 H 0 1 N N N 58.938 9.024 0.756 -6.925 3.435 -0.668 HO2 VDZ 36 VDZ H41 1H4 H 0 1 N N N 60.385 8.899 -0.809 -6.413 0.018 -1.295 H41 VDZ 37 VDZ H42 2H4 H 0 1 N N N 61.980 8.478 -0.383 -5.107 0.715 -2.289 H42 VDZ 38 VDZ H101 1H10 H 0 0 N N N 61.993 5.274 0.154 -3.809 -1.084 1.364 H101 VDZ 39 VDZ H102 2H10 H 0 0 N N N 60.492 4.643 -0.401 -5.568 -1.153 1.083 H102 VDZ 40 VDZ H6 H6 H 0 1 N N N 60.310 7.825 -2.631 -3.261 -0.643 -2.204 H6 VDZ 41 VDZ H7 H7 H 0 1 N N N 59.573 4.693 -2.596 -2.485 -1.679 0.681 H7 VDZ 42 VDZ H91 1H9 H 0 1 N N N 60.638 6.925 -5.844 -0.990 -2.560 -2.986 H91 VDZ 43 VDZ H92 2H9 H 0 1 N N N 61.379 7.398 -4.417 -1.714 -0.944 -2.837 H92 VDZ 44 VDZ H111 1H11 H 0 0 N N N 63.088 6.478 -6.132 0.669 -0.986 -3.706 H111 VDZ 45 VDZ H112 2H11 H 0 0 N N N 63.230 5.716 -4.603 0.395 0.051 -2.294 H112 VDZ 46 VDZ H14 H14 H 0 1 N N N 59.353 4.456 -5.674 0.031 -3.584 -0.655 H14 VDZ 47 VDZ H121 1H12 H 0 0 N N N 62.038 4.497 -7.196 1.575 -2.768 -2.228 H121 VDZ 48 VDZ H122 2H12 H 0 0 N N N 63.382 3.938 -6.326 2.482 -1.246 -2.018 H122 VDZ 49 VDZ H181 1H18 H 0 0 N N N 63.261 2.661 -4.285 0.488 -0.260 1.036 H181 VDZ 50 VDZ H182 2H18 H 0 0 N N N 62.408 3.994 -3.311 1.719 0.343 -0.100 H182 VDZ 51 VDZ H183 3H18 H 0 0 N N N 61.709 2.470 -3.280 0.039 0.123 -0.644 H183 VDZ 52 VDZ H151 1H15 H 0 0 N N N 59.245 2.933 -3.210 -0.628 -1.705 1.680 H151 VDZ 53 VDZ H152 2H15 H 0 0 N N N 58.104 3.240 -4.368 -0.858 -3.483 1.600 H152 VDZ 54 VDZ H161 1H16 H 0 0 N N N 59.793 0.863 -4.448 1.432 -2.305 2.657 H161 VDZ 55 VDZ H162 2H16 H 0 0 N N N 58.847 1.327 -5.749 1.436 -3.916 1.884 H162 VDZ 56 VDZ H17 H17 H 0 1 N N N 60.804 2.390 -6.986 2.696 -3.109 0.130 H17 VDZ 57 VDZ H20 H20 H 0 1 N N N 62.097 0.541 -4.989 2.480 -0.438 1.608 H20 VDZ 58 VDZ H211 1H21 H 0 0 N N N 61.659 -1.007 -6.887 3.477 -2.266 2.955 H211 VDZ 59 VDZ H212 2H21 H 0 0 N N N 59.995 -0.312 -6.385 4.621 -2.613 1.637 H212 VDZ 60 VDZ H213 3H21 H 0 0 N N N 60.643 0.273 -7.798 4.707 -1.060 2.504 H213 VDZ 61 VDZ H221 1H22 H 0 0 N N N 63.250 1.641 -7.556 4.501 -1.370 -0.478 H221 VDZ 62 VDZ H222 2H22 H 0 0 N N N 63.804 1.940 -5.983 3.156 -0.251 -0.804 H222 VDZ 63 VDZ H231 1H23 H 0 0 N N N 63.876 -0.745 -5.668 4.046 1.316 0.899 H231 VDZ 64 VDZ H232 2H23 H 0 0 N N N 63.648 -0.839 -7.360 5.392 0.197 1.225 H232 VDZ 65 VDZ H241 1H24 H 0 0 N N N 65.781 0.502 -7.784 6.135 0.405 -1.132 H241 VDZ 66 VDZ H242 2H24 H 0 0 N N N 65.984 0.790 -6.117 4.789 1.523 -1.457 H242 VDZ 67 VDZ H261 1H26 H 0 0 N N N 68.266 -2.000 -7.252 7.957 1.067 0.445 H261 VDZ 68 VDZ H262 2H26 H 0 0 N N N 67.594 -0.683 -8.395 7.909 2.658 1.242 H262 VDZ 69 VDZ H263 3H26 H 0 0 N N N 68.229 -0.156 -6.949 6.745 1.394 1.707 H263 VDZ 70 VDZ H271 1H27 H 0 0 N N N 67.111 -2.841 -5.139 6.423 3.297 -2.111 H271 VDZ 71 VDZ H272 2H27 H 0 0 N N N 66.982 -1.114 -4.568 7.720 3.770 -0.988 H272 VDZ 72 VDZ H273 3H27 H 0 0 N N N 65.533 -2.008 -4.763 7.768 2.179 -1.785 H273 VDZ 73 VDZ HO3 HO3 H 0 1 N N N 66.212 -3.123 -7.321 4.832 3.692 -0.240 HO3 VDZ 74 # # 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 VDZ O1 C1 SING N N 1 VDZ O1 HO1 SING N N 2 VDZ C1 C2 SING N N 3 VDZ C1 C10 SING N N 4 VDZ C1 H1 SING N N 5 VDZ C2 C28 DOUB N N 6 VDZ C2 C3 SING N N 7 VDZ C28 H281 SING N N 8 VDZ C28 H282 SING N N 9 VDZ C3 O2 SING N N 10 VDZ C3 C4 SING N N 11 VDZ C3 H3 SING N N 12 VDZ O2 HO2 SING N N 13 VDZ C4 C5 SING N N 14 VDZ C4 H41 SING N N 15 VDZ C4 H42 SING N N 16 VDZ C10 C5 SING N N 17 VDZ C10 H101 SING N N 18 VDZ C10 H102 SING N N 19 VDZ C5 C6 DOUB N N 20 VDZ C6 C7 SING N N 21 VDZ C6 H6 SING N N 22 VDZ C7 C8 DOUB N E 23 VDZ C7 H7 SING N N 24 VDZ C8 C9 SING N N 25 VDZ C8 C14 SING N N 26 VDZ C9 C11 SING N N 27 VDZ C9 H91 SING N N 28 VDZ C9 H92 SING N N 29 VDZ C11 C12 SING N N 30 VDZ C11 H111 SING N N 31 VDZ C11 H112 SING N N 32 VDZ C14 C13 SING N N 33 VDZ C14 C15 SING N N 34 VDZ C14 H14 SING N N 35 VDZ C13 C12 SING N N 36 VDZ C13 C18 SING N N 37 VDZ C13 C17 SING N N 38 VDZ C12 H121 SING N N 39 VDZ C12 H122 SING N N 40 VDZ C18 H181 SING N N 41 VDZ C18 H182 SING N N 42 VDZ C18 H183 SING N N 43 VDZ C15 C16 SING N N 44 VDZ C15 H151 SING N N 45 VDZ C15 H152 SING N N 46 VDZ C16 C17 SING N N 47 VDZ C16 H161 SING N N 48 VDZ C16 H162 SING N N 49 VDZ C17 C20 SING N N 50 VDZ C17 H17 SING N N 51 VDZ C20 C21 SING N N 52 VDZ C20 C22 SING N N 53 VDZ C20 H20 SING N N 54 VDZ C21 H211 SING N N 55 VDZ C21 H212 SING N N 56 VDZ C21 H213 SING N N 57 VDZ C22 C23 SING N N 58 VDZ C22 H221 SING N N 59 VDZ C22 H222 SING N N 60 VDZ C23 C24 SING N N 61 VDZ C23 H231 SING N N 62 VDZ C23 H232 SING N N 63 VDZ C24 C25 SING N N 64 VDZ C24 H241 SING N N 65 VDZ C24 H242 SING N N 66 VDZ C25 C26 SING N N 67 VDZ C25 C27 SING N N 68 VDZ C25 O3 SING N N 69 VDZ C26 H261 SING N N 70 VDZ C26 H262 SING N N 71 VDZ C26 H263 SING N N 72 VDZ C27 H271 SING N N 73 VDZ C27 H272 SING N N 74 VDZ C27 H273 SING N N 75 VDZ O3 HO3 SING N N 76 # # 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 VDZ SMILES ACDLabs 10.04 "OC3/C(=C)C(O)CC(=C\C=C1/CCCC2(C1CCC2C(C)CCCC(O)(C)C)C)\C3" VDZ InChI InChI 1.03 "InChI=1S/C27H44O3/c1-18(8-6-14-26(3,4)30)22-12-13-23-21(9-7-15-27(22,23)5)11-10-20-16-24(28)19(2)25(29)17-20/h10-11,18,22-25,28-30H,2,6-9,12-17H2,1,3-5H3/b21-11+/t18-,22+,23-,24+,25+,27+/m0/s1" VDZ InChIKey InChI 1.03 UHMPCVGLSKFXHR-NAQZCRMNSA-N VDZ SMILES_CANONICAL CACTVS 3.385 "C[C@@H](CCCC(C)(C)O)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3" VDZ SMILES CACTVS 3.385 "C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3" VDZ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "C[C@@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C" VDZ SMILES "OpenEye OEToolkits" 1.7.5 "CC(CCCC(C)(C)O)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 VDZ "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,3R,7E,17beta)-17-[(1S)-5-hydroxy-1,5-dimethylhexyl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol" VDZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2S)-6-hydroxy-6-methyl-heptan-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 VDZ "Create component" 2003-12-17 PDBJ VDZ "Modify descriptor" 2011-06-04 RCSB VDZ "Modify descriptor" 2012-01-05 RCSB VDZ "Modify coordinates" 2012-01-05 RCSB VDZ "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 VDZ "2-METHYLENE-19-NOR-(20S)-1ALPHA,25-DIHYDROXY-VITAMIN D3" ? ? 2 VDZ 2MD ? ? ##