data_VD2 # _chem_comp.id VD2 _chem_comp.name "5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYL-CYCLOHEXANE-1,3-DIOL" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H46 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-ALPHA-METHYL-19-NOR-1,25-DIHYDROXYVITAMIN D3; 2AM20R" _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 418.652 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VD2 _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 1RKH _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 VD2 O3 O3 O 0 1 N N N 65.992 -2.504 -7.436 -2.967 0.678 6.831 O3 VD2 1 VD2 C25 C25 C 0 1 N N N 66.517 -1.403 -6.745 -1.771 0.289 7.510 C25 VD2 2 VD2 C27 C27 C 0 1 N N N 67.388 -1.955 -5.566 -2.133 -0.492 8.774 C27 VD2 3 VD2 C26 C26 C 0 1 N N N 67.346 -0.512 -7.646 -0.973 1.537 7.893 C26 VD2 4 VD2 C24 C24 C 0 1 N N N 65.403 -0.624 -6.123 -0.926 -0.592 6.588 C24 VD2 5 VD2 C23 C23 C 0 1 N N N 64.551 0.217 -6.903 -0.564 0.189 5.324 C23 VD2 6 VD2 C22 C22 C 0 1 N N N 63.254 0.521 -6.194 0.280 -0.692 4.403 C22 VD2 7 VD2 C20 C20 C 0 1 N N R 62.358 1.504 -7.004 0.643 0.089 3.139 C20 VD2 8 VD2 C21 C21 C 0 1 N N N 61.534 0.610 -8.071 1.440 1.337 3.523 C21 VD2 9 VD2 C17 C17 C 0 1 N N R 61.215 2.259 -6.168 1.488 -0.792 2.218 C17 VD2 10 VD2 C16 C16 C 0 1 N N N 60.443 1.519 -4.989 0.672 -2.029 1.759 C16 VD2 11 VD2 C13 C13 C 0 1 N N R 61.754 3.544 -5.519 1.829 -0.045 0.938 C13 VD2 12 VD2 C18 C18 C 0 1 N N N 63.027 3.423 -4.433 0.657 0.860 0.557 C18 VD2 13 VD2 C14 C14 C 0 1 N N S 60.329 4.037 -4.916 1.917 -1.180 -0.121 C14 VD2 14 VD2 C15 C15 C 0 1 N N N 59.708 2.670 -4.206 0.663 -1.994 0.205 C15 VD2 15 VD2 C12 C12 C 0 1 N N N 62.226 4.755 -6.478 3.110 0.744 0.873 C12 VD2 16 VD2 C11 C11 C 0 1 N N N 62.357 6.179 -5.721 3.155 1.472 -0.480 C11 VD2 17 VD2 C9 C9 C 0 1 N N N 60.940 6.542 -5.122 3.085 0.494 -1.652 C9 VD2 18 VD2 C8 C8 C 0 1 N N N 60.562 5.320 -4.139 1.948 -0.498 -1.457 C8 VD2 19 VD2 C7 C7 C 0 1 N N N 60.498 5.405 -2.852 1.047 -0.743 -2.402 C7 VD2 20 VD2 C6 C6 C 0 1 N N N 60.719 6.664 -2.073 1.128 -0.044 -3.694 C6 VD2 21 VD2 C5 C5 C 0 1 N N N 60.883 6.793 -0.703 0.287 -0.359 -4.674 C5 VD2 22 VD2 C10 C10 C 0 1 N N N 60.942 5.589 0.250 -0.839 -1.341 -4.443 C10 VD2 23 VD2 C4 C4 C 0 1 N N N 61.058 8.144 -0.027 0.437 0.250 -6.050 C4 VD2 24 VD2 C3 C3 C 0 1 N N R 60.288 8.237 1.332 -0.913 0.833 -6.474 C3 VD2 25 VD2 O2 O2 O 0 1 N N N 58.869 8.117 1.108 -0.828 1.303 -7.821 O2 VD2 26 VD2 C2 C2 C 0 1 N N N 60.773 7.042 2.281 -1.988 -0.250 -6.378 C2 VD2 27 VD2 C28 C28 C 0 1 N N N 62.136 6.947 2.988 -3.319 0.306 -6.887 C28 VD2 28 VD2 C1 C1 C 0 1 N N R 60.331 5.684 1.679 -2.148 -0.695 -4.924 C1 VD2 29 VD2 O1 O1 O 0 1 N N N 60.813 4.594 2.524 -2.451 0.439 -4.109 O1 VD2 30 VD2 HO3 HO3 H 0 1 N N N 65.463 -2.169 -8.151 -3.439 -0.135 6.608 HO3 VD2 31 VD2 H271 1H27 H 0 0 N N N 67.805 -1.079 -5.016 -2.735 0.135 9.430 H271 VD2 32 VD2 H272 2H27 H 0 0 N N N 66.828 -2.656 -4.904 -2.701 -1.381 8.500 H272 VD2 33 VD2 H273 3H27 H 0 0 N N N 68.173 -2.669 -5.904 -1.221 -0.789 9.291 H273 VD2 34 VD2 H261 1H26 H 0 0 N N N 67.763 0.363 -7.096 -0.061 1.240 8.411 H261 VD2 35 VD2 H262 2H26 H 0 0 N N N 68.150 -1.090 -8.157 -0.715 2.094 6.993 H262 VD2 36 VD2 H263 3H26 H 0 0 N N N 66.765 -0.188 -8.541 -1.575 2.165 8.550 H263 VD2 37 VD2 H241 1H24 H 0 0 N N N 64.757 -1.338 -5.561 -1.494 -1.481 6.315 H241 VD2 38 VD2 H242 2H24 H 0 0 N N N 65.834 -0.006 -5.301 -0.014 -0.889 7.106 H242 VD2 39 VD2 H231 1H23 H 0 0 N N N 65.074 1.153 -7.207 0.004 1.078 5.598 H231 VD2 40 VD2 H232 2H23 H 0 0 N N N 64.367 -0.218 -7.913 -1.476 0.486 4.807 H232 VD2 41 VD2 H221 1H22 H 0 0 N N N 62.702 -0.414 -5.943 -0.287 -1.581 4.130 H221 VD2 42 VD2 H222 2H22 H 0 0 N N N 63.437 0.899 -5.161 1.193 -0.989 4.921 H222 VD2 43 VD2 H20 H20 H 0 1 N N N 63.053 2.272 -7.414 -0.269 0.386 2.622 H20 VD2 44 VD2 H211 1H21 H 0 0 N N N 60.892 1.313 -8.650 2.353 1.040 4.040 H211 VD2 45 VD2 H212 2H21 H 0 0 N N N 62.189 -0.021 -8.715 1.698 1.895 2.622 H212 VD2 46 VD2 H213 3H21 H 0 0 N N N 60.960 -0.221 -7.598 0.838 1.966 4.179 H213 VD2 47 VD2 H17 H17 H 0 1 N N N 60.473 2.386 -6.991 2.398 -1.107 2.727 H17 VD2 48 VD2 H161 1H16 H 0 0 N N N 59.767 0.701 -5.332 1.149 -2.943 2.111 H161 VD2 49 VD2 H162 2H16 H 0 0 N N N 61.096 0.881 -4.349 -0.347 -1.967 2.141 H162 VD2 50 VD2 H181 1H18 H 0 0 N N N 63.418 4.355 -3.962 0.809 1.246 -0.450 H181 VD2 51 VD2 H182 2H18 H 0 0 N N N 62.749 2.701 -3.629 -0.269 0.289 0.591 H182 VD2 52 VD2 H183 3H18 H 0 0 N N N 63.871 2.884 -4.924 0.597 1.692 1.259 H183 VD2 53 VD2 H14 H14 H 0 1 N N N 59.526 4.380 -5.609 2.816 -1.780 0.025 H14 VD2 54 VD2 H151 1H15 H 0 0 N N N 58.595 2.603 -4.209 0.739 -3.002 -0.204 H151 VD2 55 VD2 H152 2H15 H 0 0 N N N 59.815 2.626 -3.097 -0.230 -1.492 -0.165 H152 VD2 56 VD2 H121 1H12 H 0 0 N N N 63.179 4.496 -6.994 3.958 0.065 0.956 H121 VD2 57 VD2 H122 2H12 H 0 0 N N N 61.550 4.841 -7.361 3.137 1.471 1.685 H122 VD2 58 VD2 H111 1H11 H 0 0 N N N 63.165 6.187 -4.953 4.083 2.040 -0.547 H111 VD2 59 VD2 H112 2H11 H 0 0 N N N 62.767 6.981 -6.377 2.313 2.161 -0.542 H112 VD2 60 VD2 H91 1H9 H 0 1 N N N 60.904 7.541 -4.629 4.028 -0.048 -1.723 H91 VD2 61 VD2 H92 2H9 H 0 1 N N N 60.165 6.750 -5.896 2.922 1.050 -2.575 H92 VD2 62 VD2 H7 H7 H 0 1 N N N 60.258 4.416 -2.424 0.256 -1.456 -2.223 H7 VD2 63 VD2 H6 H6 H 0 1 N N N 60.768 7.640 -2.583 1.870 0.725 -3.846 H6 VD2 64 VD2 H101 1H10 H 0 0 N N N 60.488 4.711 -0.266 -0.655 -2.256 -5.004 H101 VD2 65 VD2 H102 2H10 H 0 0 N N N 62.006 5.269 0.344 -0.912 -1.568 -3.379 H102 VD2 66 VD2 H41 1H4 H 0 1 N N N 62.137 8.389 0.105 1.185 1.042 -6.020 H41 VD2 67 VD2 H42 2H4 H 0 1 N N N 60.767 8.975 -0.710 0.743 -0.519 -6.759 H42 VD2 68 VD2 H3 H3 H 0 1 N N N 60.497 9.222 1.809 -1.174 1.662 -5.816 H3 VD2 69 VD2 HO2 HO2 H 0 1 N N N 58.401 8.173 1.933 -0.141 1.982 -7.837 HO2 VD2 70 VD2 H2 H2 H 0 1 N N N 60.246 7.381 3.203 -1.696 -1.105 -6.988 H2 VD2 71 VD2 H281 1H28 H 0 0 N N N 62.473 6.114 3.648 -4.086 -0.465 -6.820 H281 VD2 72 VD2 H282 2H28 H 0 0 N N N 62.911 7.052 2.193 -3.611 1.162 -6.280 H282 VD2 73 VD2 H283 3H28 H 0 0 N N N 62.250 7.885 3.579 -3.209 0.618 -7.926 H283 VD2 74 VD2 H1 H1 H 0 1 N N N 59.219 5.607 1.624 -2.958 -1.421 -4.852 H1 VD2 75 VD2 HO1 HO1 H 0 1 N N N 60.440 4.652 3.395 -2.544 0.115 -3.202 HO1 VD2 76 # # 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 VD2 O3 C25 SING N N 1 VD2 O3 HO3 SING N N 2 VD2 C25 C27 SING N N 3 VD2 C25 C26 SING N N 4 VD2 C25 C24 SING N N 5 VD2 C27 H271 SING N N 6 VD2 C27 H272 SING N N 7 VD2 C27 H273 SING N N 8 VD2 C26 H261 SING N N 9 VD2 C26 H262 SING N N 10 VD2 C26 H263 SING N N 11 VD2 C24 C23 SING N N 12 VD2 C24 H241 SING N N 13 VD2 C24 H242 SING N N 14 VD2 C23 C22 SING N N 15 VD2 C23 H231 SING N N 16 VD2 C23 H232 SING N N 17 VD2 C22 C20 SING N N 18 VD2 C22 H221 SING N N 19 VD2 C22 H222 SING N N 20 VD2 C20 C21 SING N N 21 VD2 C20 C17 SING N N 22 VD2 C20 H20 SING N N 23 VD2 C21 H211 SING N N 24 VD2 C21 H212 SING N N 25 VD2 C21 H213 SING N N 26 VD2 C17 C16 SING N N 27 VD2 C17 C13 SING N N 28 VD2 C17 H17 SING N N 29 VD2 C16 C15 SING N N 30 VD2 C16 H161 SING N N 31 VD2 C16 H162 SING N N 32 VD2 C13 C18 SING N N 33 VD2 C13 C14 SING N N 34 VD2 C13 C12 SING N N 35 VD2 C18 H181 SING N N 36 VD2 C18 H182 SING N N 37 VD2 C18 H183 SING N N 38 VD2 C14 C15 SING N N 39 VD2 C14 C8 SING N N 40 VD2 C14 H14 SING N N 41 VD2 C15 H151 SING N N 42 VD2 C15 H152 SING N N 43 VD2 C12 C11 SING N N 44 VD2 C12 H121 SING N N 45 VD2 C12 H122 SING N N 46 VD2 C11 C9 SING N N 47 VD2 C11 H111 SING N N 48 VD2 C11 H112 SING N N 49 VD2 C9 C8 SING N N 50 VD2 C9 H91 SING N N 51 VD2 C9 H92 SING N N 52 VD2 C8 C7 DOUB N E 53 VD2 C7 C6 SING N N 54 VD2 C7 H7 SING N N 55 VD2 C6 C5 DOUB N N 56 VD2 C6 H6 SING N N 57 VD2 C5 C10 SING N N 58 VD2 C5 C4 SING N N 59 VD2 C10 C1 SING N N 60 VD2 C10 H101 SING N N 61 VD2 C10 H102 SING N N 62 VD2 C4 C3 SING N N 63 VD2 C4 H41 SING N N 64 VD2 C4 H42 SING N N 65 VD2 C3 O2 SING N N 66 VD2 C3 C2 SING N N 67 VD2 C3 H3 SING N N 68 VD2 O2 HO2 SING N N 69 VD2 C2 C28 SING N N 70 VD2 C2 C1 SING N N 71 VD2 C2 H2 SING N N 72 VD2 C28 H281 SING N N 73 VD2 C28 H282 SING N N 74 VD2 C28 H283 SING N N 75 VD2 C1 O1 SING N N 76 VD2 C1 H1 SING N N 77 VD2 O1 HO1 SING N N 78 # # 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 VD2 SMILES ACDLabs 10.04 "OC3CC(=C/C=C1\CCCC2(C)C(C(C)CCCC(O)(C)C)CCC12)\CC(O)C3C" VD2 SMILES_CANONICAL CACTVS 3.341 "C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2\C(CCC[C@]12C)=C\C=C/3C[C@@H](O)[C@H](C)[C@H](O)C/3" VD2 SMILES CACTVS 3.341 "C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)[CH](C)[CH](O)C3" VD2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1[C@@H](CC(=C\C=C\2/CCC[C@]3([C@H]2CC[C@@H]3[C@H](C)CCCC(C)(C)O)C)C[C@H]1O)O" VD2 SMILES "OpenEye OEToolkits" 1.5.0 "CC1C(CC(=CC=C2CCCC3(C2CCC3C(C)CCCC(C)(C)O)C)CC1O)O" VD2 InChI InChI 1.03 "InChI=1S/C27H46O3/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/h10-11,18-19,22-25,28-30H,6-9,12-17H2,1-5H3/b20-10-,21-11+/t18-,19+,22-,23+,24-,25-,27-/m1/s1" VD2 InChIKey InChI 1.03 OZPNRDQPQFOURL-VJPYOZRWSA-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 VD2 "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2R,3R,5E,7E,17beta)-17-[(1R)-5-hydroxy-1,5-dimethylhexyl]-2-methyl-9,10-secoestra-5,7-diene-1,3-diol" VD2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,3R)-5-[(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]-2-methyl-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 VD2 "Create component" 2003-12-17 EBI VD2 "Modify descriptor" 2011-06-04 RCSB VD2 "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 VD2 "2-ALPHA-METHYL-19-NOR-1,25-DIHYDROXYVITAMIN D3" ? ? 2 VD2 2AM20R ? ? ##