data_VD5 # _chem_comp.id VD5 _chem_comp.name "(1R,3R,7E,17E)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-1,3-diol" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H42 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-12-07 _chem_comp.pdbx_modified_date 2011-06-04 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 414.621 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VD5 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2O4R _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 VD5 O2 O2 O 0 1 N N N 58.641 8.112 1.129 4.747 1.111 2.503 O2 VD5 1 VD5 C3 C3 C 0 1 N N R 60.072 8.151 1.171 3.729 2.087 2.729 C3 VD5 2 VD5 C2 C2 C 0 1 N N N 60.499 6.942 1.970 4.355 3.462 2.852 C2 VD5 3 VD5 C28 C28 C 0 1 N N N 61.118 7.043 3.142 4.318 4.134 4.014 C28 VD5 4 VD5 C1 C1 C 0 1 N N R 60.155 5.610 1.429 4.964 3.994 1.567 C1 VD5 5 VD5 O1 O1 O 0 1 N N N 60.625 4.631 2.366 5.436 5.332 1.694 O1 VD5 6 VD5 C10 C10 C 0 1 N N N 60.820 5.478 0.038 3.928 3.968 0.436 C10 VD5 7 VD5 C4 C4 C 0 1 N N N 60.578 8.086 -0.267 2.725 2.029 1.568 C4 VD5 8 VD5 C5 C5 C 0 1 N N N 60.554 6.688 -0.861 3.310 2.601 0.296 C5 VD5 9 VD5 C6 C6 C 0 1 N N N 60.319 6.559 -2.204 3.302 1.930 -0.865 C6 VD5 10 VD5 C7 C7 C 0 1 N N N 60.319 5.243 -2.888 2.717 0.622 -1.019 C7 VD5 11 VD5 C8 C8 C 0 1 N N N 60.495 5.138 -4.246 2.710 -0.049 -2.180 C8 VD5 12 VD5 C9 C9 C 0 1 N N N 60.670 6.370 -5.136 3.332 0.543 -3.429 C9 VD5 13 VD5 C11 C11 C 0 1 N N N 61.924 6.213 -6.016 2.904 -0.189 -4.709 C11 VD5 14 VD5 C12 C12 C 0 1 N N N 62.156 4.798 -6.619 3.085 -1.721 -4.669 C12 VD5 15 VD5 C14 C14 C 0 1 N N R 60.607 3.814 -5.011 2.103 -1.414 -2.370 C14 VD5 16 VD5 C13 C13 C 0 1 N N S 62.039 3.680 -5.563 3.009 -2.317 -3.242 C13 VD5 17 VD5 C18 C18 C 0 1 N N N 63.138 3.765 -4.474 4.441 -2.505 -2.681 C18 VD5 18 VD5 C15 C15 C 0 1 N N N 60.283 2.458 -4.380 1.757 -2.293 -1.168 C15 VD5 19 VD5 C16 C16 C 0 1 N N N 61.031 1.433 -5.285 1.484 -3.660 -1.805 C16 VD5 20 VD5 C17 C17 C 0 1 N N N 62.080 2.235 -6.034 2.289 -3.648 -3.086 C17 VD5 21 VD5 C20 C20 C 0 1 N N N 62.926 1.715 -6.970 2.309 -4.670 -3.951 C20 VD5 22 VD5 C21 C21 C 0 1 N N N 63.968 2.533 -7.707 3.124 -4.616 -5.213 C21 VD5 23 VD5 C22 C22 C 0 1 N N N 62.889 0.263 -7.387 1.542 -5.946 -3.687 C22 VD5 24 VD5 C23 C23 C 0 1 N N N 63.767 -0.575 -6.467 2.388 -7.007 -2.973 C23 VD5 25 VD5 C24 C24 C 0 1 N N N 65.238 -0.430 -6.875 1.585 -8.297 -2.755 C24 VD5 26 VD5 C25 C25 C 0 1 N N N 66.037 -1.695 -6.622 2.369 -9.429 -2.060 C25 VD5 27 VD5 C27 C27 C 0 1 N N N 66.001 -2.175 -5.159 1.529 -10.695 -1.875 C27 VD5 28 VD5 C26 C26 C 0 1 N N N 67.482 -1.399 -6.975 2.883 -8.939 -0.702 C26 VD5 29 VD5 O3 O3 O 0 1 N N N 65.513 -2.745 -7.444 3.503 -9.752 -2.868 O3 VD5 30 VD5 HO2 HO2 H 0 1 N N N 58.298 8.103 2.015 4.299 0.251 2.457 HO2 VD5 31 VD5 H3 H3 H 0 1 N N N 60.475 9.063 1.635 3.220 1.803 3.657 H3 VD5 32 VD5 H281 1H28 H 0 0 N N N 61.240 8.100 3.330 3.867 3.693 4.895 H281 VD5 33 VD5 H282 2H28 H 0 0 N N N 61.436 6.231 3.779 4.738 5.131 4.091 H282 VD5 34 VD5 H1 H1 H 0 1 N N N 59.073 5.464 1.297 5.828 3.374 1.298 H1 VD5 35 VD5 HO1 HO1 H 0 1 N N N 60.729 3.795 1.926 5.206 5.783 0.867 HO1 VD5 36 VD5 H101 1H10 H 0 0 N N N 60.416 4.582 -0.457 4.404 4.288 -0.501 H101 VD5 37 VD5 H102 2H10 H 0 0 N N N 61.907 5.409 0.193 3.138 4.706 0.630 H102 VD5 38 VD5 H41 1H4 H 0 1 N N N 61.618 8.444 -0.279 1.829 2.607 1.827 H41 VD5 39 VD5 H42 2H4 H 0 1 N N N 59.905 8.708 -0.875 2.411 0.991 1.405 H42 VD5 40 VD5 H6 H6 H 0 1 N N N 60.127 7.448 -2.786 3.758 2.390 -1.737 H6 VD5 41 VD5 H7 H7 H 0 1 N N N 60.177 4.346 -2.304 2.260 0.160 -0.149 H7 VD5 42 VD5 H91 1H9 H 0 1 N N N 60.780 7.263 -4.503 3.070 1.604 -3.518 H91 VD5 43 VD5 H92 2H9 H 0 1 N N N 59.787 6.476 -5.783 4.424 0.480 -3.340 H92 VD5 44 VD5 H111 1H11 H 0 0 N N N 62.797 6.451 -5.390 1.844 0.029 -4.896 H111 VD5 45 VD5 H112 2H11 H 0 0 N N N 61.778 6.887 -6.873 3.450 0.218 -5.569 H112 VD5 46 VD5 H121 1H12 H 0 0 N N N 61.399 4.623 -7.398 2.323 -2.164 -5.321 H121 VD5 47 VD5 H122 2H12 H 0 0 N N N 63.177 4.770 -7.027 4.050 -1.978 -5.125 H122 VD5 48 VD5 H14 H14 H 0 1 N N N 59.779 3.955 -5.721 1.152 -1.246 -2.905 H14 VD5 49 VD5 H181 1H18 H 0 0 N N N 64.128 3.785 -4.952 4.679 -1.713 -1.964 H181 VD5 50 VD5 H182 2H18 H 0 0 N N N 62.998 4.682 -3.883 4.531 -3.469 -2.173 H182 VD5 51 VD5 H183 3H18 H 0 0 N N N 63.068 2.888 -3.814 5.177 -2.471 -3.489 H183 VD5 52 VD5 H151 1H15 H 0 0 N N N 59.199 2.269 -4.372 0.888 -1.925 -0.613 H151 VD5 53 VD5 H152 2H15 H 0 0 N N N 60.596 2.398 -3.327 2.599 -2.360 -0.467 H152 VD5 54 VD5 H161 1H16 H 0 0 N N N 60.334 0.952 -5.987 0.418 -3.760 -2.036 H161 VD5 55 VD5 H162 2H16 H 0 0 N N N 61.486 0.627 -4.691 1.785 -4.470 -1.134 H162 VD5 56 VD5 H211 1H21 H 0 0 N N N 63.622 2.731 -8.732 2.478 -4.669 -6.095 H211 VD5 57 VD5 H212 2H21 H 0 0 N N N 64.124 3.487 -7.182 3.706 -3.691 -5.285 H212 VD5 58 VD5 H213 3H21 H 0 0 N N N 64.915 1.974 -7.742 3.829 -5.452 -5.247 H213 VD5 59 VD5 H221 1H22 H 0 0 N N N 61.853 -0.103 -7.330 0.652 -5.712 -3.089 H221 VD5 60 VD5 H222 2H22 H 0 0 N N N 63.266 0.177 -8.417 1.170 -6.363 -4.632 H222 VD5 61 VD5 H231 1H23 H 0 0 N N N 63.641 -0.230 -5.430 2.733 -6.620 -2.007 H231 VD5 62 VD5 H232 2H23 H 0 0 N N N 63.471 -1.631 -6.547 3.280 -7.218 -3.575 H232 VD5 63 VD5 H241 1H24 H 0 0 N N N 65.684 0.387 -6.289 0.711 -8.047 -2.138 H241 VD5 64 VD5 H242 2H24 H 0 0 N N N 65.269 -0.223 -7.955 1.205 -8.651 -3.721 H242 VD5 65 VD5 H271 1H27 H 0 0 N N N 65.992 -3.275 -5.133 1.278 -11.153 -2.838 H271 VD5 66 VD5 H272 2H27 H 0 0 N N N 66.890 -1.803 -4.629 0.603 -10.487 -1.329 H272 VD5 67 VD5 H273 3H27 H 0 0 N N N 65.094 -1.790 -4.669 2.091 -11.455 -1.320 H273 VD5 68 VD5 H261 1H26 H 0 0 N N N 67.586 -1.327 -8.068 3.536 -8.067 -0.824 H261 VD5 69 VD5 H262 2H26 H 0 0 N N N 67.784 -0.447 -6.515 2.060 -8.666 -0.034 H262 VD5 70 VD5 H263 3H26 H 0 0 N N N 68.124 -2.209 -6.598 3.488 -9.710 -0.210 H263 VD5 71 VD5 HO3 HO3 H 0 1 N N N 65.397 -2.425 -8.331 3.306 -9.424 -3.758 HO3 VD5 72 # 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 VD5 C21 C20 SING N N 1 VD5 O3 C25 SING N N 2 VD5 C22 C20 SING N N 3 VD5 C22 C23 SING N N 4 VD5 C26 C25 SING N N 5 VD5 C20 C17 DOUB N E 6 VD5 C24 C25 SING N N 7 VD5 C24 C23 SING N N 8 VD5 C25 C27 SING N N 9 VD5 C12 C11 SING N N 10 VD5 C12 C13 SING N N 11 VD5 C17 C13 SING N N 12 VD5 C17 C16 SING N N 13 VD5 C11 C9 SING N N 14 VD5 C13 C14 SING N N 15 VD5 C13 C18 SING N N 16 VD5 C16 C15 SING N N 17 VD5 C9 C8 SING N N 18 VD5 C14 C15 SING N N 19 VD5 C14 C8 SING N N 20 VD5 C8 C7 DOUB N E 21 VD5 C7 C6 SING N N 22 VD5 C6 C5 DOUB N N 23 VD5 C5 C4 SING N N 24 VD5 C5 C10 SING N N 25 VD5 C4 C3 SING N N 26 VD5 C10 C1 SING N N 27 VD5 O2 C3 SING N N 28 VD5 C3 C2 SING N N 29 VD5 C1 C2 SING N N 30 VD5 C1 O1 SING N N 31 VD5 C2 C28 DOUB N N 32 VD5 O2 HO2 SING N N 33 VD5 C3 H3 SING N N 34 VD5 C28 H281 SING N N 35 VD5 C28 H282 SING N N 36 VD5 C1 H1 SING N N 37 VD5 O1 HO1 SING N N 38 VD5 C10 H101 SING N N 39 VD5 C10 H102 SING N N 40 VD5 C4 H41 SING N N 41 VD5 C4 H42 SING N N 42 VD5 C6 H6 SING N N 43 VD5 C7 H7 SING N N 44 VD5 C9 H91 SING N N 45 VD5 C9 H92 SING N N 46 VD5 C11 H111 SING N N 47 VD5 C11 H112 SING N N 48 VD5 C12 H121 SING N N 49 VD5 C12 H122 SING N N 50 VD5 C14 H14 SING N N 51 VD5 C18 H181 SING N N 52 VD5 C18 H182 SING N N 53 VD5 C18 H183 SING N N 54 VD5 C15 H151 SING N N 55 VD5 C15 H152 SING N N 56 VD5 C16 H161 SING N N 57 VD5 C16 H162 SING N N 58 VD5 C21 H211 SING N N 59 VD5 C21 H212 SING N N 60 VD5 C21 H213 SING N N 61 VD5 C22 H221 SING N N 62 VD5 C22 H222 SING N N 63 VD5 C23 H231 SING N N 64 VD5 C23 H232 SING N N 65 VD5 C24 H241 SING N N 66 VD5 C24 H242 SING N N 67 VD5 C27 H271 SING N N 68 VD5 C27 H272 SING N N 69 VD5 C27 H273 SING N N 70 VD5 C26 H261 SING N N 71 VD5 C26 H262 SING N N 72 VD5 C26 H263 SING N N 73 VD5 O3 HO3 SING N N 74 # 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 VD5 SMILES ACDLabs 10.04 "OC3\C(=C)C(O)CC(=C\C=C1/CCCC2(C(=C(/C)CCCC(O)(C)C)\CCC12)C)\C3" VD5 SMILES_CANONICAL CACTVS 3.341 "C\C(CCCC(C)(C)O)=C/1CC[C@H]2C(\CCC[C@]/12C)=C\C=C/3C[C@@H](O)C(=C)[C@H](O)C/3" VD5 SMILES CACTVS 3.341 "CC(CCCC(C)(C)O)=C1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3" VD5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C/C(=C\1/CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C)/CCCC(C)(C)O" VD5 SMILES "OpenEye OEToolkits" 1.5.0 "CC(=C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C)CCCC(C)(C)O" VD5 InChI InChI 1.03 "InChI=1S/C27H42O3/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/h10-11,23-25,28-30H,2,6-9,12-17H2,1,3-5H3/b21-11+,22-18+/t23-,24+,25+,27+/m0/s1" VD5 InChIKey InChI 1.03 PCPYFQNISYYIPU-QEWVMUDDSA-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 VD5 "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,3R,7E,17E)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol" VD5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,3R)-5-[(2E)-2-[(1E,3aS,7aS)-1-(6-hydroxy-6-methyl-heptan-2-ylidene)-7a-methyl-2,3,3a,5,6,7-hexahydroinden-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 VD5 "Create component" 2006-12-07 EBI VD5 "Modify descriptor" 2011-06-04 RCSB #