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                                            ?  ?  
##
