data_VD3
#

_chem_comp.id                                   VD3
_chem_comp.name                                 
;(1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI
DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C27 H44 O"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "VITAMIN D3"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2006-06-15
_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                       384.638
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VD3
_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       ?
_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
VD3  O     O     O  0  1  N  N  N  -0.432   0.185  24.583  -5.539  -3.548  -0.709  O     VD3   1  
VD3  C1    C1    C  0  1  N  N  N   0.634   1.412  21.416  -7.115  -0.429   0.671  C1    VD3   2  
VD3  C2    C2    C  0  1  N  N  N   0.289   1.765  22.818  -6.855  -1.930   0.507  C2    VD3   3  
VD3  C3    C3    C  0  1  N  N  S  -0.929   0.981  23.494  -5.680  -2.151  -0.447  C3    VD3   4  
VD3  C4    C4    C  0  1  N  N  N  -1.633   0.070  22.460  -4.391  -1.618   0.185  C4    VD3   5  
VD3  C5    C5    C  0  1  N  N  N  -1.876   0.751  21.032  -4.587  -0.149   0.505  C5    VD3   6  
VD3  C7    C7    C  0  1  N  N  N  -3.094   0.632  20.405  -3.656   0.774   0.185  C7    VD3   7  
VD3  C8    C8    C  0  1  N  N  N  -4.496   1.237  20.391  -2.421   0.366  -0.488  C8    VD3   8  
VD3  C9    C9    C  0  1  N  N  N  -4.760   2.544  19.971  -1.502   1.278  -0.804  C9    VD3   9  
VD3  C10   C10   C  0  1  N  N  N  -4.835   2.045  18.426  -1.680   2.758  -0.492  C10   VD3  10  
VD3  C6    C6    C  0  1  N  N  N  -0.619   1.528  20.525  -5.843   0.221   1.189  C6    VD3  11  
VD3  C11   C11   C  0  1  N  N  N  -4.361   2.992  17.372  -0.448   3.313   0.219  C11   VD3  12  
VD3  C12   C12   C  0  1  N  N  N  -4.501   4.544  17.630   0.852   2.920  -0.504  C12   VD3  13  
VD3  C13   C13   C  0  1  N  N  R  -4.181   4.992  19.057   0.923   1.417  -0.558  C13   VD3  14  
VD3  C14   C14   C  0  1  N  N  S  -3.760   3.797  19.985  -0.218   0.921  -1.492  C14   VD3  15  
VD3  C15   C15   C  0  1  N  N  N  -3.510   4.548  21.388   0.110  -0.570  -1.603  C15   VD3  16  
VD3  C16   C16   C  0  1  N  N  N  -2.940   6.012  20.970   1.656  -0.569  -1.769  C16   VD3  17  
VD3  C17   C17   C  0  1  N  N  R  -2.873   5.914  19.400   2.162   0.757  -1.144  C17   VD3  18  
VD3  C18   C18   C  0  1  N  N  N  -5.554   5.695  19.498   0.664   0.848   0.839  C18   VD3  19  
VD3  C19   C19   C  0  1  N  N  N  -0.577   2.209  19.448  -5.863   1.087   2.202  C19   VD3  20  
VD3  C20   C20   C  0  1  N  N  R  -2.899   7.364  18.620   3.183   0.469  -0.041  C20   VD3  21  
VD3  C21   C21   C  0  1  N  N  N  -1.521   7.511  17.986   3.615   1.784   0.610  C21   VD3  22  
VD3  C22   C22   C  0  1  N  N  N  -3.007   8.707  19.437   4.404  -0.226  -0.646  C22   VD3  23  
VD3  C23   C23   C  0  1  N  N  N  -4.241   9.651  18.788   5.369  -0.626   0.472  C23   VD3  24  
VD3  C24   C24   C  0  1  N  N  N  -3.387  10.910  18.467   6.590  -1.321  -0.133  C24   VD3  25  
VD3  C25   C25   C  0  1  N  N  N  -3.686  12.301  19.059   7.556  -1.721   0.985  C25   VD3  26  
VD3  C26   C26   C  0  1  N  N  N  -2.338  12.451  19.433   8.715  -2.525   0.394  C26   VD3  27  
VD3  C27   C27   C  0  1  N  N  N  -3.671  13.599  18.440   8.101  -0.462   1.662  C27   VD3  28  
VD3  HO    HO    H  0  1  N  N  N  -0.322  -0.714  24.295  -4.793  -3.645  -1.316  HO    VD3  29  
VD3  H11   1H1   H  0  1  N  N  N   1.009   0.378  21.383  -7.388   0.004  -0.291  H11   VD3  30  
VD3  H12   2H1   H  0  1  N  N  N   1.409   2.100  21.047  -7.922  -0.273   1.387  H12   VD3  31  
VD3  H21   1H2   H  0  1  N  N  N  -0.033   2.816  22.778  -7.746  -2.410   0.102  H21   VD3  32  
VD3  H22   2H2   H  0  1  N  N  N   1.181   1.560  23.429  -6.620  -2.366   1.478  H22   VD3  33  
VD3  H3    H3    H  0  1  N  N  N  -1.661   1.712  23.868  -5.869  -1.624  -1.383  H3    VD3  34  
VD3  H41   1H4   H  0  1  N  N  N  -2.626  -0.165  22.871  -3.563  -1.735  -0.514  H41   VD3  35  
VD3  H42   2H4   H  0  1  N  N  N  -1.001  -0.817  22.307  -4.177  -2.168   1.102  H42   VD3  36  
VD3  H7    H7    H  0  1  N  N  N  -3.041  -0.160  19.672  -3.823   1.814   0.424  H7    VD3  37  
VD3  H8    H8    H  0  1  N  N  N  -5.323   0.626  20.721  -2.254  -0.674  -0.727  H8    VD3  38  
VD3  H101  1H10  H  0  0  N  N  N  -5.907   1.905  18.223  -1.835   3.304  -1.422  H101  VD3  39  
VD3  H102  2H10  H  0  0  N  N  N  -4.209   1.144  18.351  -2.553   2.887   0.149  H102  VD3  40  
VD3  H111  1H11  H  0  0  N  N  N  -5.020   2.797  16.513  -0.519   4.400   0.256  H111  VD3  41  
VD3  H112  2H11  H  0  0  N  N  N  -3.288   2.794  17.233  -0.419   2.924   1.237  H112  VD3  42  
VD3  H121  1H12  H  0  0  N  N  N  -5.558   4.795  17.455   0.846   3.318  -1.518  H121  VD3  43  
VD3  H122  2H12  H  0  0  N  N  N  -3.803   5.060  16.953   1.711   3.311   0.042  H122  VD3  44  
VD3  H14   H14   H  0  1  N  N  N  -2.862   3.254  19.654  -0.157   1.403  -2.468  H14   VD3  45  
VD3  H151  1H15  H  0  0  N  N  N  -2.811   3.998  22.035  -0.372  -1.008  -2.476  H151  VD3  46  
VD3  H152  2H15  H  0  0  N  N  N  -4.443   4.635  21.964  -0.180  -1.098  -0.694  H152  VD3  47  
VD3  H161  1H16  H  0  0  N  N  N  -1.972   6.252  21.434   1.918  -0.608  -2.827  H161  VD3  48  
VD3  H162  2H16  H  0  0  N  N  N  -3.606   6.822  21.302   2.090  -1.420  -1.244  H162  VD3  49  
VD3  H17   H17   H  0  1  N  N  N  -1.919   5.492  19.051   2.603   1.393  -1.911  H17   VD3  50  
VD3  H181  1H18  H  0  0  N  N  N  -6.401   5.048  19.226  -0.321   1.165   1.183  H181  VD3  51  
VD3  H182  2H18  H  0  0  N  N  N  -5.652   6.663  18.985   0.702  -0.240   0.801  H182  VD3  52  
VD3  H183  3H18  H  0  0  N  N  N  -5.551   5.856  20.586   1.425   1.215   1.528  H183  VD3  53  
VD3  H191  1H19  H  0  0  N  N  N  -1.374   2.365  18.736  -6.799   1.341   2.677  H191  VD3  54  
VD3  H192  2H19  H  0  0  N  N  N   0.430   2.596  19.404  -4.943   1.534   2.549  H192  VD3  55  
VD3  H20   H20   H  0  1  N  N  N  -3.808   7.291  18.005   2.732  -0.178   0.712  H20   VD3  56  
VD3  H211  1H21  H  0  0  N  N  N  -0.894   6.652  18.268   4.066   2.431  -0.143  H211  VD3  57  
VD3  H212  2H21  H  0  0  N  N  N  -1.052   8.440  18.341   2.745   2.280   1.041  H212  VD3  58  
VD3  H213  3H21  H  0  0  N  N  N  -1.622   7.546  16.891   4.342   1.579   1.395  H213  VD3  59  
VD3  H221  1H22  H  0  0  N  N  N  -2.054   9.253  19.378   4.906   0.454  -1.333  H221  VD3  60  
VD3  H222  2H22  H  0  0  N  N  N  -3.231   8.481  20.490   4.084  -1.118  -1.186  H222  VD3  61  
VD3  H231  1H23  H  0  0  N  N  N  -5.117   9.813  19.434   4.867  -1.307   1.159  H231  VD3  62  
VD3  H232  2H23  H  0  0  N  N  N  -4.720   9.205  17.904   5.689   0.265   1.012  H232  VD3  63  
VD3  H241  1H24  H  0  0  N  N  N  -3.601  11.065  17.399   7.093  -0.640  -0.820  H241  VD3  64  
VD3  H242  2H24  H  0  0  N  N  N  -2.371  10.664  18.809   6.271  -2.212  -0.673  H242  VD3  65  
VD3  H25   H25   H  0  1  N  N  N  -4.677  12.210  19.527   7.029  -2.329   1.720  H25   VD3  66  
VD3  H261  1H26  H  0  0  N  N  N  -2.033  11.597  20.056   9.403  -2.809   1.191  H261  VD3  67  
VD3  H262  2H26  H  0  0  N  N  N  -2.218  13.383  20.005   8.327  -3.422  -0.088  H262  VD3  68  
VD3  H263  3H26  H  0  0  N  N  N  -1.709  12.490  18.531   9.243  -1.916  -0.340  H263  VD3  69  
VD3  H271  1H27  H  0  0  N  N  N  -4.565  13.715  17.810   7.274   0.111   2.083  H271  VD3  70  
VD3  H272  2H27  H  0  0  N  N  N  -2.769  13.698  17.818   8.788  -0.746   2.459  H272  VD3  71  
VD3  H273  3H27  H  0  0  N  N  N  -3.667  14.377  19.218   8.628   0.147   0.928  H273  VD3  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
VD3  O    C3    SING  N  N   1  
VD3  O    HO    SING  N  N   2  
VD3  C1   C2    SING  N  N   3  
VD3  C1   C6    SING  N  N   4  
VD3  C1   H11   SING  N  N   5  
VD3  C1   H12   SING  N  N   6  
VD3  C2   C3    SING  N  N   7  
VD3  C2   H21   SING  N  N   8  
VD3  C2   H22   SING  N  N   9  
VD3  C3   C4    SING  N  N  10  
VD3  C3   H3    SING  N  N  11  
VD3  C4   C5    SING  N  N  12  
VD3  C4   H41   SING  N  N  13  
VD3  C4   H42   SING  N  N  14  
VD3  C5   C7    DOUB  N  E  15  
VD3  C5   C6    SING  N  N  16  
VD3  C7   C8    SING  N  N  17  
VD3  C7   H7    SING  N  N  18  
VD3  C8   C9    DOUB  N  Z  19  
VD3  C8   H8    SING  N  N  20  
VD3  C9   C10   SING  N  N  21  
VD3  C9   C14   SING  N  N  22  
VD3  C10  C11   SING  N  N  23  
VD3  C10  H101  SING  N  N  24  
VD3  C10  H102  SING  N  N  25  
VD3  C6   C19   DOUB  N  N  26  
VD3  C11  C12   SING  N  N  27  
VD3  C11  H111  SING  N  N  28  
VD3  C11  H112  SING  N  N  29  
VD3  C12  C13   SING  N  N  30  
VD3  C12  H121  SING  N  N  31  
VD3  C12  H122  SING  N  N  32  
VD3  C13  C14   SING  N  N  33  
VD3  C13  C17   SING  N  N  34  
VD3  C13  C18   SING  N  N  35  
VD3  C14  C15   SING  N  N  36  
VD3  C14  H14   SING  N  N  37  
VD3  C15  C16   SING  N  N  38  
VD3  C15  H151  SING  N  N  39  
VD3  C15  H152  SING  N  N  40  
VD3  C16  C17   SING  N  N  41  
VD3  C16  H161  SING  N  N  42  
VD3  C16  H162  SING  N  N  43  
VD3  C17  C20   SING  N  N  44  
VD3  C17  H17   SING  N  N  45  
VD3  C18  H181  SING  N  N  46  
VD3  C18  H182  SING  N  N  47  
VD3  C18  H183  SING  N  N  48  
VD3  C19  H191  SING  N  N  49  
VD3  C19  H192  SING  N  N  50  
VD3  C20  C21   SING  N  N  51  
VD3  C20  C22   SING  N  N  52  
VD3  C20  H20   SING  N  N  53  
VD3  C21  H211  SING  N  N  54  
VD3  C21  H212  SING  N  N  55  
VD3  C21  H213  SING  N  N  56  
VD3  C22  C23   SING  N  N  57  
VD3  C22  H221  SING  N  N  58  
VD3  C22  H222  SING  N  N  59  
VD3  C23  C24   SING  N  N  60  
VD3  C23  H231  SING  N  N  61  
VD3  C23  H232  SING  N  N  62  
VD3  C24  C25   SING  N  N  63  
VD3  C24  H241  SING  N  N  64  
VD3  C24  H242  SING  N  N  65  
VD3  C25  C26   SING  N  N  66  
VD3  C25  C27   SING  N  N  67  
VD3  C25  H25   SING  N  N  68  
VD3  C26  H261  SING  N  N  69  
VD3  C26  H262  SING  N  N  70  
VD3  C26  H263  SING  N  N  71  
VD3  C27  H271  SING  N  N  72  
VD3  C27  H272  SING  N  N  73  
VD3  C27  H273  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
VD3  SMILES            ACDLabs               10.04  "OC3CC(=C/C=C1\CCCC2(C)C(C(C)CCCC(C)C)CCC12)\C(=C)CC3"  
VD3  SMILES_CANONICAL  CACTVS                3.341  "CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C\C=C3/C[C@@H](O)CCC3=C"  
VD3  SMILES            CACTVS                3.341  "CC(C)CCC[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)CCC3=C"  
VD3  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CCCC2=CC=C3C[C@H](CCC3=C)O)C"  
VD3  SMILES            "OpenEye OEToolkits"  1.5.0  "CC(C)CCCC(C)C1CCC2C1(CCCC2=CC=C3CC(CCC3=C)O)C"  
VD3  InChI             InChI                 1.03   "InChI=1S/C27H44O/c1-19(2)8-6-9-21(4)25-15-16-26-22(10-7-17-27(25,26)5)12-13-23-18-24(28)14-11-20(23)3/h12-13,19,21,24-26,28H,3,6-11,14-18H2,1-2,4-5H3/t21-,24+,25-,26+,27-/m1/s1"  
VD3  InChIKey          InChI                 1.03   QYSXJUFSXHHAJI-RWDMXNMGSA-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
VD3  "SYSTEMATIC NAME"  ACDLabs               10.04  "(3S,5E,7Z,14beta,17alpha)-9,10-secocholesta-5,7,10-trien-3-ol"  
VD3  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(1S)-3-[2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methylheptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VD3  "Create component"   2006-06-15  EBI   
VD3  "Modify descriptor"  2011-06-04  RCSB  
VD3  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VD3
_pdbx_chem_comp_synonyms.name        "VITAMIN D3"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
