data_VDB
#

_chem_comp.id                                   VDB
_chem_comp.name                                 "(1R,2S,3R,5Z,7E)-17-{(1R)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C28 H46 O5 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "(20R)-1alpha,25-dihydroxy-2beta-(2-hydroxyethoxy)-16-ene-22-thia-26,27-dimethyl-19,24-dinorvitamin D3"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2008-04-09
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       494.727
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VDB
_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       2ZLA
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
VDB  C29   C29   C  0  1  N  N  N   7.708  -0.703  29.648   10.066  -1.877   0.073  C29   VDB   1  
VDB  C26   C26   C  0  1  N  N  N   8.339   0.463  28.866    8.944  -1.166   0.834  C26   VDB   2  
VDB  C25   C25   C  0  1  N  N  N   9.388   0.108  27.776    7.626  -1.340   0.078  C25   VDB   3  
VDB  C27   C27   C  0  1  N  N  N   8.728  -0.677  26.603    7.794  -0.847  -1.361  C27   VDB   4  
VDB  C28   C28   C  0  1  N  N  N   7.597   0.012  25.814    8.156   0.639  -1.352  C28   VDB   5  
VDB  O3    O3    O  0  1  N  N  N  10.417  -0.676  28.379    7.260  -2.721   0.069  O3    VDB   6  
VDB  C23   C23   C  0  1  N  N  N   9.931   1.470  27.326    6.530  -0.526   0.770  C23   VDB   7  
VDB  S22   S22   S  0  1  N  N  N  11.054   2.400  28.436    5.002  -0.620  -0.202  S22   VDB   8  
VDB  C20   C20   C  0  1  N  N  R  12.751   1.734  28.102    3.842   0.388   0.762  C20   VDB   9  
VDB  C21   C21   C  0  1  N  N  N  13.702   1.898  29.302    3.590  -0.280   2.116  C21   VDB  10  
VDB  C17   C17   C  0  1  N  N  N  13.390   2.429  26.839    2.540   0.511   0.013  C17   VDB  11  
VDB  C16   C16   C  0  1  N  N  N  14.169   1.796  25.931    2.203  -0.175  -1.071  C16   VDB  12  
VDB  C15   C15   C  0  1  N  N  N  14.642   2.781  24.837    0.827   0.259  -1.569  C15   VDB  13  
VDB  C14   C14   C  0  1  N  N  S  14.617   4.042  25.705    0.694   1.667  -0.985  C14   VDB  14  
VDB  C13   C13   C  0  1  N  N  S  13.250   3.933  26.458    1.421   1.413   0.369  C13   VDB  15  
VDB  C18   C18   C  0  1  N  N  N  11.906   4.076  25.632    0.454   0.608   1.239  C18   VDB  16  
VDB  C12   C12   C  0  1  N  N  N  13.304   5.002  27.607    1.625   2.731   1.055  C12   VDB  17  
VDB  C11   C11   C  0  1  N  N  N  13.539   6.466  27.087    0.236   3.255   1.467  C11   VDB  18  
VDB  C9    C9    C  0  1  N  N  N  14.702   6.580  26.065   -0.705   3.383   0.272  C9    VDB  19  
VDB  C8    C8    C  0  1  N  N  N  14.626   5.461  25.014   -0.680   2.124  -0.586  C8    VDB  20  
VDB  C7    C7    C  0  1  N  N  N  14.518   5.646  23.647   -1.785   1.478  -0.940  C7    VDB  21  
VDB  C6    C6    C  0  1  N  N  N  14.459   6.736  22.779   -3.100   1.982  -0.514  C6    VDB  22  
VDB  C5    C5    C  0  1  N  N  N  14.323   6.903  21.417   -4.199   1.286  -0.787  C5    VDB  23  
VDB  C10   C10   C  0  1  N  N  N  14.186   5.726  20.443   -5.568   1.838  -0.459  C10   VDB  24  
VDB  C1    C1    C  0  1  N  N  R  14.760   6.002  19.046   -6.342   0.782   0.337  C1    VDB  25  
VDB  O1    O1    O  0  1  N  N  N  14.386   4.900  18.223   -7.681   1.232   0.549  O1    VDB  26  
VDB  C4    C4    C  0  1  N  N  N  14.288   8.357  20.884   -4.112  -0.076  -1.439  C4    VDB  27  
VDB  C3    C3    C  0  1  N  N  R  14.718   8.509  19.398   -4.935  -1.067  -0.609  C3    VDB  28  
VDB  O2    O2    O  0  1  N  N  N  16.142   8.523  19.425   -4.337  -1.222   0.680  O2    VDB  29  
VDB  C2    C2    C  0  1  N  N  N  14.195   7.341  18.473   -6.363  -0.531  -0.447  C2    VDB  30  
VDB  O4    O4    O  0  1  N  N  N  14.566   7.624  17.089   -7.156  -1.490   0.254  O4    VDB  31  
VDB  C30   C30   C  0  1  N  N  N  13.449   8.187  16.359   -7.804  -2.440  -0.594  C30   VDB  32  
VDB  C31   C31   C  0  1  N  N  N  13.967   8.152  14.915   -8.621  -3.413   0.259  C31   VDB  33  
VDB  O5    O5    O  0  1  N  N  N  13.713   6.899  14.286   -9.678  -2.704   0.909  O5    VDB  34  
VDB  H29   H29   H  0  1  N  N  N   7.557  -1.559  28.973   11.005  -1.753   0.611  H29   VDB  35  
VDB  H29A  H29A  H  0  0  N  N  N   8.377  -0.998  30.470    9.832  -2.938  -0.011  H29A  VDB  36  
VDB  H29B  H29B  H  0  0  N  N  N   6.738  -0.386  30.060   10.158  -1.446  -0.924  H29B  VDB  37  
VDB  H26   H26   H  0  1  N  N  N   7.517   0.990  28.360    8.851  -1.598   1.830  H26   VDB  38  
VDB  H26A  H26A  H  0  0  N  N  N   8.893   1.045  29.617    9.178  -0.105   0.917  H26A  VDB  39  
VDB  H27   H27   H  0  1  N  N  N   9.528  -0.898  25.881    8.589  -1.412  -1.848  H27   VDB  40  
VDB  H27A  H27A  H  0  0  N  N  N   8.247  -1.542  27.082    6.860  -0.991  -1.906  H27A  VDB  41  
VDB  H28   H28   H  0  1  N  N  N   6.734   0.176  26.476    7.392   1.196  -0.810  H28   VDB  42  
VDB  H28A  H28A  H  0  0  N  N  N   7.954   0.979  25.431    9.121   0.775  -0.864  H28A  VDB  43  
VDB  H28B  H28B  H  0  0  N  N  N   7.296  -0.628  24.972    8.212   1.005  -2.378  H28B  VDB  44  
VDB  HO3   HO3   H  0  1  N  N  N  11.098  -0.850  27.740    7.136  -3.101   0.949  HO3   VDB  45  
VDB  H23   H23   H  0  1  N  N  N  10.495   1.287  26.399    6.352  -0.931   1.766  H23   VDB  46  
VDB  H23A  H23A  H  0  0  N  N  N   9.035   2.105  27.260    6.846   0.513   0.851  H23A  VDB  47  
VDB  H20   H20   H  0  1  N  N  N  12.624   0.658  27.914    4.266   1.380   0.920  H20   VDB  48  
VDB  H21   H21   H  0  1  N  N  N  14.741   1.937  28.944    3.166  -1.271   1.959  H21   VDB  49  
VDB  H21A  H21A  H  0  0  N  N  N  13.462   2.830  29.835    4.532  -0.369   2.658  H21A  VDB  50  
VDB  H21B  H21B  H  0  0  N  N  N  13.581   1.044  29.984    2.894   0.326   2.696  H21B  VDB  51  
VDB  H16   H16   H  0  1  N  N  N  14.425   0.747  25.966    2.816  -0.932  -1.537  H16   VDB  52  
VDB  H15   H15   H  0  1  N  N  N  15.633   2.545  24.422    0.800   0.287  -2.658  H15   VDB  53  
VDB  H15A  H15A  H  0  0  N  N  N  14.046   2.810  23.913    0.049  -0.397  -1.178  H15A  VDB  54  
VDB  H14   H14   H  0  1  N  N  N  15.554   4.036  26.281    1.212   2.405  -1.598  H14   VDB  55  
VDB  H18   H18   H  0  1  N  N  N  11.052   4.109  26.324    0.912   0.418   2.210  H18   VDB  56  
VDB  H18A  H18A  H  0  0  N  N  N  11.936   5.004  25.042   -0.467   1.174   1.377  H18A  VDB  57  
VDB  H18B  H18B  H  0  0  N  N  N  11.797   3.214  24.957    0.229  -0.340   0.751  H18B  VDB  58  
VDB  H12   H12   H  0  1  N  N  N  12.344   4.978  28.143    2.247   2.596   1.940  H12   VDB  59  
VDB  H12A  H12A  H  0  0  N  N  N  14.156   4.744  28.254    2.099   3.435   0.372  H12A  VDB  60  
VDB  H11   H11   H  0  1  N  N  N  12.616   6.808  26.596   -0.201   2.568   2.191  H11   VDB  61  
VDB  H11A  H11A  H  0  0  N  N  N  13.808   7.082  27.958    0.351   4.234   1.934  H11A  VDB  62  
VDB  H9    H9    H  0  1  N  N  N  14.636   7.553  25.556   -1.720   3.555   0.632  H9    VDB  63  
VDB  H9A   H9A   H  0  1  N  N  N  15.655   6.488  26.607   -0.396   4.232  -0.339  H9A   VDB  64  
VDB  H7    H7    H  0  1  N  N  N  14.466   4.706  23.117   -1.719   0.584  -1.541  H7    VDB  65  
VDB  H6    H6    H  0  1  N  N  N  14.539   7.678  23.300   -3.173   2.918   0.021  H6    VDB  66  
VDB  H10   H10   H  0  1  N  N  N  14.726   4.868  20.869   -5.464   2.744   0.138  H10   VDB  67  
VDB  H10A  H10A  H  0  0  N  N  N  13.110   5.538  20.316   -6.102   2.065  -1.382  H10A  VDB  68  
VDB  H1    H1    H  0  1  N  N  N  15.854   6.107  19.084   -5.855   0.624   1.299  H1    VDB  69  
VDB  HO1   HO1   H  0  1  N  N  N  14.303   5.191  17.322   -7.744   2.062   1.041  HO1   VDB  70  
VDB  H4    H4    H  0  1  N  N  N  13.255   8.724  20.975   -4.513  -0.024  -2.451  H4    VDB  71  
VDB  H4A   H4A   H  0  1  N  N  N  15.011   8.930  21.482   -3.072  -0.401  -1.470  H4A   VDB  72  
VDB  H3    H3    H  0  1  N  N  N  14.285   9.424  18.968   -4.962  -2.031  -1.115  H3    VDB  73  
VDB  HO2   HO2   H  0  1  N  N  N  16.476   8.526  18.536   -3.430  -1.556   0.655  HO2   VDB  74  
VDB  H2    H2    H  0  1  N  N  N  13.099   7.253  18.467   -6.793  -0.357  -1.433  H2    VDB  75  
VDB  H30   H30   H  0  1  N  N  N  12.531   7.593  16.484   -8.466  -1.919  -1.285  H30   VDB  76  
VDB  H30A  H30A  H  0  0  N  N  N  13.159   9.192  16.700   -7.054  -2.994  -1.158  H30A  VDB  77  
VDB  H31   H31   H  0  1  N  N  N  13.461   8.942  14.341   -9.043  -4.190  -0.378  H31   VDB  78  
VDB  H31A  H31A  H  0  0  N  N  N  15.056   8.306  14.940   -7.975  -3.869   1.009  H31A  VDB  79  
VDB  HO5   HO5   H  0  1  N  N  N  13.656   7.022  13.346  -10.238  -3.259   1.468  HO5   VDB  80  
#   #
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
VDB  C29  C26   SING  N  N   1  
VDB  C26  C25   SING  N  N   2  
VDB  C25  C27   SING  N  N   3  
VDB  C25  O3    SING  N  N   4  
VDB  C25  C23   SING  N  N   5  
VDB  C27  C28   SING  N  N   6  
VDB  C23  S22   SING  N  N   7  
VDB  S22  C20   SING  N  N   8  
VDB  C20  C21   SING  N  N   9  
VDB  C20  C17   SING  N  N  10  
VDB  C17  C16   DOUB  N  N  11  
VDB  C17  C13   SING  N  N  12  
VDB  C16  C15   SING  N  N  13  
VDB  C15  C14   SING  N  N  14  
VDB  C14  C13   SING  N  N  15  
VDB  C14  C8    SING  N  N  16  
VDB  C13  C18   SING  N  N  17  
VDB  C13  C12   SING  N  N  18  
VDB  C12  C11   SING  N  N  19  
VDB  C11  C9    SING  N  N  20  
VDB  C9   C8    SING  N  N  21  
VDB  C8   C7    DOUB  N  N  22  
VDB  C7   C6    SING  N  N  23  
VDB  C6   C5    DOUB  N  N  24  
VDB  C5   C10   SING  N  N  25  
VDB  C5   C4    SING  N  N  26  
VDB  C10  C1    SING  N  N  27  
VDB  C1   O1    SING  N  N  28  
VDB  C1   C2    SING  N  N  29  
VDB  C4   C3    SING  N  N  30  
VDB  C3   O2    SING  N  N  31  
VDB  C3   C2    SING  N  N  32  
VDB  C2   O4    SING  N  N  33  
VDB  O4   C30   SING  N  N  34  
VDB  C30  C31   SING  N  N  35  
VDB  C31  O5    SING  N  N  36  
VDB  C29  H29   SING  N  N  37  
VDB  C29  H29A  SING  N  N  38  
VDB  C29  H29B  SING  N  N  39  
VDB  C26  H26   SING  N  N  40  
VDB  C26  H26A  SING  N  N  41  
VDB  C27  H27   SING  N  N  42  
VDB  C27  H27A  SING  N  N  43  
VDB  C28  H28   SING  N  N  44  
VDB  C28  H28A  SING  N  N  45  
VDB  C28  H28B  SING  N  N  46  
VDB  O3   HO3   SING  N  N  47  
VDB  C23  H23   SING  N  N  48  
VDB  C23  H23A  SING  N  N  49  
VDB  C20  H20   SING  N  N  50  
VDB  C21  H21   SING  N  N  51  
VDB  C21  H21A  SING  N  E  52  
VDB  C21  H21B  SING  N  N  53  
VDB  C16  H16   SING  N  N  54  
VDB  C15  H15   SING  N  N  55  
VDB  C15  H15A  SING  N  N  56  
VDB  C14  H14   SING  N  N  57  
VDB  C18  H18   SING  N  N  58  
VDB  C18  H18A  SING  N  N  59  
VDB  C18  H18B  SING  N  N  60  
VDB  C12  H12   SING  N  N  61  
VDB  C12  H12A  SING  N  N  62  
VDB  C11  H11   SING  N  N  63  
VDB  C11  H11A  SING  N  N  64  
VDB  C9   H9    SING  N  N  65  
VDB  C9   H9A   SING  N  N  66  
VDB  C7   H7    SING  N  N  67  
VDB  C6   H6    SING  N  N  68  
VDB  C10  H10   SING  N  N  69  
VDB  C10  H10A  SING  N  N  70  
VDB  C1   H1    SING  N  N  71  
VDB  O1   HO1   SING  N  N  72  
VDB  C4   H4    SING  N  N  73  
VDB  C4   H4A   SING  N  N  74  
VDB  C3   H3    SING  N  N  75  
VDB  O2   HO2   SING  N  N  76  
VDB  C2   H2    SING  N  N  77  
VDB  C30  H30   SING  N  N  78  
VDB  C30  H30A  SING  N  N  79  
VDB  C31  H31   SING  N  N  80  
VDB  C31  H31A  SING  N  N  81  
VDB  O5   HO5   SING  N  N  82  
#   #
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
VDB  SMILES            ACDLabs               10.04  "O(CCO)C3C(O)C/C(=C/C=C1\CCCC2(C(=CCC12)C(SCC(O)(CC)CC)C)C)CC3O"  
VDB  SMILES_CANONICAL  CACTVS                3.341  "CCC(O)(CC)CS[C@H](C)C1=CC[C@H]2\C(CCC[C@]12C)=C\C=C3/C[C@@H](O)[C@H](OCCO)[C@H](O)C3"  
VDB  SMILES            CACTVS                3.341  "CCC(O)(CC)CS[CH](C)C1=CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)[CH](OCCO)[CH](O)C3"  
VDB  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CCC(CC)(CS[C@H](C)C1=CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C([C@@H](C3)O)OCCO)O)C)O"  
VDB  SMILES            "OpenEye OEToolkits"  1.5.0  "CCC(CC)(CSC(C)C1=CCC2C1(CCCC2=CC=C3CC(C(C(C3)O)OCCO)O)C)O"  
VDB  InChI             InChI                 1.03   "InChI=1S/C28H46O5S/c1-5-28(32,6-2)18-34-19(3)22-11-12-23-21(8-7-13-27(22,23)4)10-9-20-16-24(30)26(25(31)17-20)33-15-14-29/h9-11,19,23-26,29-32H,5-8,12-18H2,1-4H3/b20-9-,21-10+/t19-,23+,24-,25-,26-,27-/m1/s1"  
VDB  InChIKey          InChI                 1.03   DUIYWCMQVXJTIP-XXAWZNHHSA-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
VDB  "SYSTEMATIC NAME"  ACDLabs               10.04  "(1R,2S,3R,5Z,7E)-17-{(1R)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol"  
VDB  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(1R,3R)-5-[(2E)-2-[(3aS,7aS)-1-[(1R)-1-(2-ethyl-2-hydroxy-butyl)sulfanylethyl]-7a-methyl-3a,5,6,7-tetrahydro-3H-inden-4-ylidene]ethylidene]-2-(2-hydroxyethoxy)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
VDB  "Create component"   2008-04-09  PDBJ  
VDB  "Modify descriptor"  2011-06-04  RCSB  
VDB  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VDB
_pdbx_chem_comp_synonyms.name        "(20R)-1alpha,25-dihydroxy-2beta-(2-hydroxyethoxy)-16-ene-22-thia-26,27-dimethyl-19,24-dinorvitamin D3"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
