data_VD1
#

_chem_comp.id                                   VD1
_chem_comp.name                                 "5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C23 H36 O2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "1-ALPHA-HYDROXY-2-METHYLENE-19-NOR-(20S)-BISHOMOPREGNACALCIFEROL; 2MBISP"
_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                       344.531
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VD1
_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       1RKG
_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
VD1  O2    O2    O  0  1  N  N  N  58.937   8.128   1.083   5.251  -1.514  -0.870  O2    VD1   1  
VD1  C3    C3    C  0  1  N  N  R  60.437   8.098   1.175   5.276  -0.983   0.456  C3    VD1   2  
VD1  C2    C2    C  0  1  N  N  N  60.695   6.869   2.009   5.439   0.519   0.399  C2    VD1   3  
VD1  C28   C28   C  0  1  N  N  N  61.359   7.021   3.137   6.512   1.092   0.884  C28   VD1   4  
VD1  C1    C1    C  0  1  N  N  R  60.264   5.525   1.564   4.341   1.347  -0.228  C1    VD1   5  
VD1  O1    O1    O  0  1  N  N  N  60.781   4.400   2.318   4.641   2.736  -0.075  O1    VD1   6  
VD1  C4    C4    C  0  1  N  N  N  60.939   7.994  -0.229   3.954  -1.306   1.165  C4    VD1   7  
VD1  C5    C5    C  0  1  N  N  N  60.753   6.639  -0.805   2.856  -0.477   0.538  C5    VD1   8  
VD1  C10   C10   C  0  1  N  N  N  60.857   5.418   0.138   3.019   1.025   0.481  C10   VD1   9  
VD1  C6    C6    C  0  1  N  N  N  60.486   6.662  -2.189   1.768  -1.058   0.045  C6    VD1  10  
VD1  C7    C7    C  0  1  N  N  N  60.284   5.418  -2.984   0.651  -0.235  -0.442  C7    VD1  11  
VD1  C8    C8    C  0  1  N  N  N  60.492   5.312  -4.296  -0.478  -0.813  -0.838  C8    VD1  12  
VD1  C9    C9    C  0  1  N  N  N  61.001   6.426  -5.170  -0.674  -2.322  -0.810  C9    VD1  13  
VD1  C11   C11   C  0  1  N  N  N  62.360   5.999  -5.733  -1.983  -2.684  -0.110  C11   VD1  14  
VD1  C12   C12   C  0  1  N  N  N  62.297   4.645  -6.496  -3.163  -1.853  -0.642  C12   VD1  15  
VD1  C13   C13   C  0  1  N  N  R  61.727   3.566  -5.556  -2.836  -0.397  -0.409  C13   VD1  16  
VD1  C18   C18   C  0  1  N  N  N  62.812   3.320  -4.368  -2.408  -0.201   1.047  C18   VD1  17  
VD1  C14   C14   C  0  1  N  N  S  60.288   3.958  -4.964  -1.652  -0.025  -1.339  C14   VD1  18  
VD1  C15   C15   C  0  1  N  N  N  59.665   2.729  -4.352  -1.592   1.492  -1.150  C15   VD1  19  
VD1  C17   C17   C  0  1  N  N  R  61.383   2.179  -6.139  -3.884   0.645  -0.769  C17   VD1  20  
VD1  C16   C16   C  0  1  N  N  N  60.269   1.576  -5.213  -3.093   1.899  -1.166  C16   VD1  21  
VD1  C20   C20   C  0  1  N  N  S  62.497   1.217  -6.581  -4.759   0.960   0.445  C20   VD1  22  
VD1  C21   C21   C  0  1  N  N  N  61.749   0.165  -7.432  -5.805   2.009   0.062  C21   VD1  23  
VD1  C22   C22   C  0  1  N  N  N  63.631   1.891  -7.406  -5.463  -0.316   0.911  C22   VD1  24  
VD1  C23   C23   C  0  1  N  N  N  65.026   1.668  -6.831  -6.240  -0.029   2.198  C23   VD1  25  
VD1  HO2   HO2   H  0  1  N  N  N  58.774   8.902   0.557   6.052  -1.334  -1.381  HO2   VD1  26  
VD1  H3    H3    H  0  1  N  N  N  60.939   8.982   1.632   6.107  -1.420   1.010  H3    VD1  27  
VD1  H281  1H28  H  0  0  N  N  N  61.680   8.022   3.468   7.291   0.491   1.329  H281  VD1  28  
VD1  H282  2H28  H  0  0  N  N  N  61.547   6.121   3.747   6.619   2.166   0.838  H282  VD1  29  
VD1  H1    H1    H  0  1  N  N  N  59.156   5.457   1.671   4.259   1.106  -1.288  H1    VD1  30  
VD1  HO1   HO1   H  0  1  N  N  N  60.504   3.537   2.032   5.472   3.007  -0.488  HO1   VD1  31  
VD1  H41   1H4   H  0  1  N  N  N  60.474   8.772  -0.878   3.725  -2.365   1.048  H41   VD1  32  
VD1  H42   2H4   H  0  1  N  N  N  62.004   8.314  -0.297   4.038  -1.061   2.224  H42   VD1  33  
VD1  H101  1H10  H  0  0  N  N  N  61.926   5.111   0.214   3.038   1.430   1.492  H101  VD1  34  
VD1  H102  2H10  H  0  0  N  N  N  60.413   4.530  -0.371   2.190   1.462  -0.075  H102  VD1  35  
VD1  H6    H6    H  0  1  N  N  N  60.434   7.661  -2.653   1.703  -2.135   0.003  H6    VD1  36  
VD1  H7    H7    H  0  1  N  N  N  59.940   4.463  -2.550   0.748   0.840  -0.479  H7    VD1  37  
VD1  H91   1H9   H  0  1  N  N  N  60.275   6.716  -5.965  -0.697  -2.700  -1.832  H91   VD1  38  
VD1  H92   2H9   H  0  1  N  N  N  61.041   7.406  -4.640   0.157  -2.782  -0.276  H92   VD1  39  
VD1  H111  1H11  H  0  0  N  N  N  62.795   6.799  -6.375  -2.191  -3.741  -0.272  H111  VD1  40  
VD1  H112  2H11  H  0  0  N  N  N  63.133   5.969  -4.930  -1.875  -2.504   0.960  H112  VD1  41  
VD1  H121  1H12  H  0  0  N  N  N  61.725   4.721  -7.450  -3.294  -2.037  -1.708  H121  VD1  42  
VD1  H122  2H12  H  0  0  N  N  N  63.283   4.354  -6.927  -4.074  -2.118  -0.105  H122  VD1  43  
VD1  H181  1H18  H  0  0  N  N  N  62.399   2.539  -3.687  -1.535  -0.819   1.256  H181  VD1  44  
VD1  H182  2H18  H  0  0  N  N  N  63.826   3.065  -4.754  -2.160   0.847   1.215  H182  VD1  45  
VD1  H183  3H18  H  0  0  N  N  N  63.088   4.258  -3.832  -3.225  -0.491   1.708  H183  VD1  46  
VD1  H14   H14   H  0  1  N  N  N  59.425   4.196  -5.628  -1.877  -0.284  -2.373  H14   VD1  47  
VD1  H151  1H15  H  0  0  N  N  N  59.820   2.623  -3.253  -1.134   1.744  -0.193  H151  VD1  48  
VD1  H152  2H15  H  0  0  N  N  N  58.551   2.743  -4.304  -1.055   1.963  -1.973  H152  VD1  49  
VD1  H17   H17   H  0  1  N  N  N  61.019   2.349  -7.179  -4.497   0.294  -1.599  H17   VD1  50  
VD1  H161  1H16  H  0  0  N  N  N  60.640   0.727  -4.592  -3.269   2.710  -0.459  H161  VD1  51  
VD1  H162  2H16  H  0  0  N  N  N  59.492   1.017  -5.785  -3.386   2.208  -2.170  H162  VD1  52  
VD1  H20   H20   H  0  1  N  N  N  63.031   0.795  -5.697  -4.136   1.346   1.252  H20   VD1  53  
VD1  H211  1H21  H  0  0  N  N  N  62.557  -0.533  -7.752  -6.429   2.233   0.927  H211  VD1  54  
VD1  H212  2H21  H  0  0  N  N  N  60.893  -0.326  -6.912  -5.304   2.918  -0.270  H212  VD1  55  
VD1  H213  3H21  H  0  0  N  N  N  61.147   0.590  -8.268  -6.428   1.622  -0.745  H213  VD1  56  
VD1  H221  1H22  H  0  0  N  N  N  63.588   1.565  -8.471  -6.153  -0.653   0.138  H221  VD1  57  
VD1  H222  2H22  H  0  0  N  N  N  63.428   2.979  -7.535  -4.721  -1.092   1.100  H222  VD1  58  
VD1  H231  1H23  H  0  0  N  N  N  65.838   2.151  -7.422  -5.549   0.308   2.971  H231  VD1  59  
VD1  H232  2H23  H  0  0  N  N  N  65.068   1.993  -5.765  -6.981   0.747   2.010  H232  VD1  60  
VD1  H233  3H23  H  0  0  N  N  N  65.228   0.579  -6.701  -6.741  -0.938   2.530  H233  VD1  61  
#   #
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
VD1  O2   C3    SING  N  N   1  
VD1  O2   HO2   SING  N  N   2  
VD1  C3   C2    SING  N  N   3  
VD1  C3   C4    SING  N  N   4  
VD1  C3   H3    SING  N  N   5  
VD1  C2   C28   DOUB  N  N   6  
VD1  C2   C1    SING  N  N   7  
VD1  C28  H281  SING  N  N   8  
VD1  C28  H282  SING  N  N   9  
VD1  C1   O1    SING  N  N  10  
VD1  C1   C10   SING  N  N  11  
VD1  C1   H1    SING  N  N  12  
VD1  O1   HO1   SING  N  N  13  
VD1  C4   C5    SING  N  N  14  
VD1  C4   H41   SING  N  N  15  
VD1  C4   H42   SING  N  N  16  
VD1  C5   C10   SING  N  N  17  
VD1  C5   C6    DOUB  N  N  18  
VD1  C10  H101  SING  N  N  19  
VD1  C10  H102  SING  N  N  20  
VD1  C6   C7    SING  N  N  21  
VD1  C6   H6    SING  N  N  22  
VD1  C7   C8    DOUB  N  E  23  
VD1  C7   H7    SING  N  N  24  
VD1  C8   C9    SING  N  N  25  
VD1  C8   C14   SING  N  N  26  
VD1  C9   C11   SING  N  N  27  
VD1  C9   H91   SING  N  N  28  
VD1  C9   H92   SING  N  N  29  
VD1  C11  C12   SING  N  N  30  
VD1  C11  H111  SING  N  N  31  
VD1  C11  H112  SING  N  N  32  
VD1  C12  C13   SING  N  N  33  
VD1  C12  H121  SING  N  N  34  
VD1  C12  H122  SING  N  N  35  
VD1  C13  C18   SING  N  N  36  
VD1  C13  C14   SING  N  N  37  
VD1  C13  C17   SING  N  N  38  
VD1  C18  H181  SING  N  N  39  
VD1  C18  H182  SING  N  N  40  
VD1  C18  H183  SING  N  N  41  
VD1  C14  C15   SING  N  N  42  
VD1  C14  H14   SING  N  N  43  
VD1  C15  C16   SING  N  N  44  
VD1  C15  H151  SING  N  N  45  
VD1  C15  H152  SING  N  N  46  
VD1  C17  C16   SING  N  N  47  
VD1  C17  C20   SING  N  N  48  
VD1  C17  H17   SING  N  N  49  
VD1  C16  H161  SING  N  N  50  
VD1  C16  H162  SING  N  N  51  
VD1  C20  C21   SING  N  N  52  
VD1  C20  C22   SING  N  N  53  
VD1  C20  H20   SING  N  N  54  
VD1  C21  H211  SING  N  N  55  
VD1  C21  H212  SING  N  N  56  
VD1  C21  H213  SING  N  N  57  
VD1  C22  C23   SING  N  N  58  
VD1  C22  H221  SING  N  N  59  
VD1  C22  H222  SING  N  N  60  
VD1  C23  H231  SING  N  N  61  
VD1  C23  H232  SING  N  N  62  
VD1  C23  H233  SING  N  N  63  
#   #
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
VD1  SMILES            ACDLabs               10.04  "OC3\C(=C)C(O)CC(=C\C=C1/CCCC2(C1CCC2C(C)CC)C)\C3"  
VD1  InChI             InChI                 1.03   "InChI=1S/C23H36O2/c1-5-15(2)19-10-11-20-18(7-6-12-23(19,20)4)9-8-17-13-21(24)16(3)22(25)14-17/h8-9,15,19-22,24-25H,3,5-7,10-14H2,1-2,4H3/b18-9+/t15-,19+,20-,21+,22+,23+/m0/s1"  
VD1  InChIKey          InChI                 1.03   QSLUXQQUPXBIHH-YHSKWIAJSA-N  
VD1  SMILES_CANONICAL  CACTVS                3.385  "CC[C@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3"  
VD1  SMILES            CACTVS                3.385  "CC[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3"  
VD1  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.5  "CC[C@H](C)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C"  
VD1  SMILES            "OpenEye OEToolkits"  1.7.5  "CCC(C)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
VD1  "SYSTEMATIC NAME"  ACDLabs               10.04  "(1R,3R,7E,17beta)-2-methylidene-17-[(1S)-1-methylpropyl]-9,10-secoestra-5,7-diene-1,3-diol"  
VD1  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2S)-butan-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
VD1  "Create component"    2003-12-17  EBI   
VD1  "Modify descriptor"   2011-06-04  RCSB  
VD1  "Modify descriptor"   2012-01-05  RCSB  
VD1  "Modify coordinates"  2012-01-05  RCSB  
VD1  "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  VD1  "1-ALPHA-HYDROXY-2-METHYLENE-19-NOR-(20S)-BISHOMOPREGNACALCIFEROL"  ?  ?  
2  VD1  2MBISP                                                              ?  ?  
##
