data_VDA
#

_chem_comp.id                                   VDA
_chem_comp.name                                 "(1R,2R,3R,5Z)-17-{(1S)-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                        "(20S)-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                    VDA
_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       2ZL9
_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
VDA  O2    O2    O  0  1  N  N  N  16.341   8.598  19.342    6.511   1.467   0.718  O2    VDA   1  
VDA  C1    C1    C  0  1  N  N  R  14.808   6.038  19.069    5.293  -1.082   0.352  C1    VDA   2  
VDA  C2    C2    C  0  1  N  N  N  14.284   7.441  18.444    6.490  -0.628  -0.485  C2    VDA   3  
VDA  C3    C3    C  0  1  N  N  R  14.911   8.713  19.348    6.500   0.897  -0.592  C3    VDA   4  
VDA  C4    C4    C  0  1  N  N  N  14.394   8.548  20.899    5.247   1.363  -1.342  C4    VDA   5  
VDA  C5    C5    C  0  1  N  N  N  14.551   7.136  21.544    4.031   0.795  -0.645  C5    VDA   6  
VDA  C6    C6    C  0  1  N  N  N  14.434   6.930  22.870    3.020   1.581  -0.291  C6    VDA   7  
VDA  C7    C7    C  0  1  N  N  N  14.950   5.820  23.721    1.791   0.993   0.266  C7    VDA   8  
VDA  C8    C8    C  0  1  N  N  N  14.727   5.701  24.946    0.743   1.768   0.525  C8    VDA   9  
VDA  C9    C9    C  0  1  N  N  N  14.513   6.971  26.034    0.742   3.271   0.271  C9    VDA  10  
VDA  C10   C10   C  0  1  N  N  N  14.254   5.919  20.542    3.995  -0.690  -0.362  C10   VDA  11  
VDA  C11   C11   C  0  1  N  N  N  13.256   6.821  27.019   -0.475   3.687  -0.552  C11   VDA  12  
VDA  C12   C12   C  0  1  N  N  N  13.092   5.250  27.577   -1.780   3.086   0.001  C12   VDA  13  
VDA  C13   C13   C  0  1  N  N  S  13.302   4.041  26.408   -1.613   1.595   0.024  C13   VDA  14  
VDA  C14   C14   C  0  1  N  N  S  14.728   4.352  25.728   -0.544   1.235   1.087  C14   VDA  15  
VDA  C15   C15   C  0  1  N  N  N  15.217   2.898  25.026   -0.741  -0.283   1.082  C15   VDA  16  
VDA  C16   C16   C  0  1  N  N  N  14.366   1.844  25.787   -2.246  -0.419   0.870  C16   VDA  17  
VDA  C17   C17   C  0  1  N  N  N  13.624   2.598  26.944   -2.730   0.665   0.301  C17   VDA  18  
VDA  C18   C18   C  0  1  N  N  N  11.938   4.196  25.417   -1.029   1.184  -1.329  C18   VDA  19  
VDA  C20   C20   C  0  1  N  N  S  12.798   2.164  28.343   -4.181   0.911  -0.027  C20   VDA  20  
VDA  C21   C21   C  0  1  N  N  N  13.549   0.791  28.732   -4.731   2.010   0.885  C21   VDA  21  
VDA  S22   S22   S  0  1  N  N  N  11.124   2.228  28.324   -5.126  -0.616   0.228  S22   VDA  22  
VDA  C23   C23   C  0  1  N  N  N  10.551   1.217  27.346   -6.785  -0.172  -0.355  C23   VDA  23  
VDA  C25   C25   C  0  1  N  N  N   9.335   0.372  27.818   -7.718  -1.375  -0.204  C25   VDA  24  
VDA  O3    O3    O  0  1  N  N  N  10.242  -0.752  28.394   -7.875  -1.685   1.182  O3    VDA  25  
VDA  C26   C26   C  0  1  N  N  N   8.236   0.757  28.508   -9.083  -1.041  -0.809  C26   VDA  26  
VDA  C27   C27   C  0  1  N  N  N   9.195  -0.373  26.391   -7.118  -2.580  -0.931  C27   VDA  27  
VDA  O1    O1    O  0  1  N  N  N  14.389   4.919  18.298    5.337  -2.500   0.518  O1    VDA  28  
VDA  O4    O4    O  0  1  N  N  N  14.625   7.620  17.080    7.699  -1.069   0.137  O4    VDA  29  
VDA  C30   C30   C  0  1  N  N  N  13.538   8.121  16.456    8.764  -1.326  -0.780  C30   VDA  30  
VDA  C31   C31   C  0  1  N  N  N  14.128   8.244  14.878   10.001  -1.789  -0.007  C31   VDA  31  
VDA  O5    O5    O  0  1  N  N  N  13.768   6.985  14.292    9.729  -3.045   0.619  O5    VDA  32  
VDA  C29   C29   C  0  1  N  N  N   7.387   1.974  27.706   -9.650   0.208  -0.131  C29   VDA  33  
VDA  C28   C28   C  0  1  N  N  N   8.167  -1.624  26.236   -8.052  -3.783  -0.782  C28   VDA  34  
VDA  HO2   HO2   H  0  1  N  N  N  16.653   8.573  18.445    6.517   2.434   0.726  HO2   VDA  35  
VDA  H1    H1    H  0  1  N  N  N  15.908   6.035  19.062    5.330  -0.600   1.329  H1    VDA  36  
VDA  H2    H2    H  0  1  N  N  N  13.185   7.420  18.491    6.419  -1.061  -1.483  H2    VDA  37  
VDA  H3    H3    H  0  1  N  N  N  14.592   9.680  18.933    7.389   1.218  -1.135  H3    VDA  38  
VDA  H4    H4    H  0  1  N  N  N  14.978   9.251  21.512    5.199   2.452  -1.333  H4    VDA  39  
VDA  H4A   H4A   H  0  1  N  N  N  13.311   8.738  20.869    5.281   1.003  -2.371  H4A   VDA  40  
VDA  H6    H6    H  0  1  N  N  N  13.878   7.689  23.401    3.100   2.651  -0.411  H6    VDA  41  
VDA  H7    H7    H  0  1  N  N  N  15.559   5.065  23.246    1.741  -0.067   0.463  H7    VDA  42  
VDA  H9    H9    H  0  1  N  N  N  15.418   7.032  26.656    0.724   3.795   1.227  H9    VDA  43  
VDA  H9A   H9A   H  0  1  N  N  N  14.325   7.869  25.427    1.649   3.543  -0.268  H9A   VDA  44  
VDA  H10   H10   H  0  1  N  N  N  13.160   5.827  20.466    3.913  -1.240  -1.299  H10   VDA  45  
VDA  H10A  H10A  H  0  0  N  N  N  14.780   5.056  20.976    3.142  -0.920   0.277  H10A  VDA  46  
VDA  H11   H11   H  0  1  N  N  N  13.400   7.489  27.881   -0.554   4.774  -0.542  H11   VDA  47  
VDA  H11A  H11A  H  0  0  N  N  N  12.346   7.085  26.460   -0.338   3.353  -1.580  H11A  VDA  48  
VDA  H12   H12   H  0  1  N  N  N  13.852   5.093  28.357   -1.959   3.454   1.011  H12   VDA  49  
VDA  H12A  H12A  H  0  0  N  N  N  12.056   5.157  27.933   -2.615   3.355  -0.646  H12A  VDA  50  
VDA  H14   H14   H  0  1  N  N  N  15.550   4.614  26.411   -0.770   1.679   2.056  H14   VDA  51  
VDA  H15   H15   H  0  1  N  N  N  15.017   2.880  23.945   -0.191  -0.742   0.261  H15   VDA  52  
VDA  H15A  H15A  H  0  0  N  N  N  16.300   2.721  25.108   -0.444  -0.714   2.038  H15A  VDA  53  
VDA  H16   H16   H  0  1  N  N  N  14.298   0.790  25.561   -2.833  -1.280   1.154  H16   VDA  54  
VDA  H18   H18   H  0  1  N  N  N  11.033   4.230  26.041   -0.061   1.666  -1.469  H18   VDA  55  
VDA  H18A  H18A  H  0  0  N  N  N  12.014   5.124  24.831   -0.903   0.102  -1.357  H18A  VDA  56  
VDA  H18B  H18B  H  0  0  N  N  N  11.881   3.335  24.735   -1.706   1.492  -2.126  H18B  VDA  57  
VDA  H20   H20   H  0  1  N  N  N  12.855   2.909  29.151   -4.270   1.224  -1.067  H20   VDA  58  
VDA  H21   H21   H  0  1  N  N  N  13.720   0.196  27.823   -4.642   1.696   1.926  H21   VDA  59  
VDA  H21A  H21A  H  0  0  N  N  N  14.515   1.023  29.205   -4.163   2.927   0.732  H21A  VDA  60  
VDA  H21B  H21B  H  0  0  N  N  N  12.925   0.218  29.433   -5.780   2.187   0.648  H21B  VDA  61  
VDA  H23   H23   H  0  1  N  N  N  10.224   1.780  26.459   -7.167   0.661   0.236  H23   VDA  62  
VDA  H23A  H23A  H  0  0  N  N  N  11.359   0.488  27.183   -6.735   0.120  -1.404  H23A  VDA  63  
VDA  HO3   HO3   H  0  1  N  N  N  10.427  -1.390  27.715   -8.251  -0.964   1.706  HO3   VDA  64  
VDA  H26   H26   H  0  1  N  N  N   7.574  -0.113  28.631   -8.970  -0.855  -1.878  H26   VDA  65  
VDA  H26A  H26A  H  0  0  N  N  N   8.563   1.151  29.482   -9.763  -1.879  -0.656  H26A  VDA  66  
VDA  H27   H27   H  0  1  N  N  N   8.858   0.392  25.676   -6.997  -2.343  -1.988  H27   VDA  67  
VDA  H27A  H27A  H  0  0  N  N  N  10.185  -0.824  26.230   -6.146  -2.818  -0.499  H27A  VDA  68  
VDA  HO1   HO1   H  0  1  N  N  N  14.296   5.178  17.389    4.606  -2.858   1.040  HO1   VDA  69  
VDA  H30   H30   H  0  1  N  N  N  12.663   7.459  16.531    8.461  -2.105  -1.480  H30   VDA  70  
VDA  H30A  H30A  H  0  0  N  N  N  13.162   9.064  16.879    8.999  -0.415  -1.329  H30A  VDA  71  
VDA  H31   H31   H  0  1  N  N  N  13.670   9.087  14.339   10.839  -1.900  -0.696  H31   VDA  72  
VDA  H31A  H31A  H  0  0  N  N  N  15.210   8.440  14.840   10.252  -1.050   0.754  H31A  VDA  73  
VDA  HO5   HO5   H  0  1  N  N  N  13.688   7.085  13.351   10.472  -3.399   1.128  HO5   VDA  74  
VDA  H29   H29   H  0  1  N  N  N   7.202   2.809  28.397   -9.677   0.054   0.948  H29   VDA  75  
VDA  H29A  H29A  H  0  0  N  N  N   7.979   2.331  26.850   -9.017   1.065  -0.360  H29A  VDA  76  
VDA  H29B  H29B  H  0  0  N  N  N   6.426   1.576  27.348  -10.660   0.393  -0.498  H29B  VDA  77  
VDA  H28   H28   H  0  1  N  N  N   7.935  -1.779  25.172   -8.246  -3.962   0.276  H28   VDA  78  
VDA  H28A  H28A  H  0  0  N  N  N   8.631  -2.533  26.646   -8.992  -3.578  -1.294  H28A  VDA  79  
VDA  H28B  H28B  H  0  0  N  N  N   7.239  -1.406  26.785   -7.583  -4.663  -1.220  H28B  VDA  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
VDA  O2   C3    SING  N  N   1  
VDA  C1   C2    SING  N  N   2  
VDA  C1   C10   SING  N  N   3  
VDA  C1   O1    SING  N  N   4  
VDA  C2   C3    SING  N  N   5  
VDA  C2   O4    SING  N  N   6  
VDA  C3   C4    SING  N  N   7  
VDA  C4   C5    SING  N  N   8  
VDA  C5   C6    DOUB  N  N   9  
VDA  C5   C10   SING  N  N  10  
VDA  C6   C7    SING  N  N  11  
VDA  C7   C8    DOUB  N  N  12  
VDA  C8   C9    SING  N  N  13  
VDA  C8   C14   SING  N  N  14  
VDA  C9   C11   SING  N  N  15  
VDA  C11  C12   SING  N  N  16  
VDA  C12  C13   SING  N  N  17  
VDA  C13  C14   SING  N  N  18  
VDA  C13  C17   SING  N  E  19  
VDA  C13  C18   SING  N  N  20  
VDA  C14  C15   SING  N  N  21  
VDA  C15  C16   SING  N  N  22  
VDA  C16  C17   DOUB  N  N  23  
VDA  C17  C20   SING  N  N  24  
VDA  C20  C21   SING  N  N  25  
VDA  C20  S22   SING  N  N  26  
VDA  S22  C23   SING  N  N  27  
VDA  C23  C25   SING  N  N  28  
VDA  C25  O3    SING  N  N  29  
VDA  C25  C26   SING  N  N  30  
VDA  C25  C27   SING  N  N  31  
VDA  C26  C29   SING  N  N  32  
VDA  C27  C28   SING  N  N  33  
VDA  O4   C30   SING  N  N  34  
VDA  C30  C31   SING  N  N  35  
VDA  C31  O5    SING  N  N  36  
VDA  O2   HO2   SING  N  N  37  
VDA  C1   H1    SING  N  N  38  
VDA  C2   H2    SING  N  N  39  
VDA  C3   H3    SING  N  N  40  
VDA  C4   H4    SING  N  N  41  
VDA  C4   H4A   SING  N  N  42  
VDA  C6   H6    SING  N  N  43  
VDA  C7   H7    SING  N  N  44  
VDA  C9   H9    SING  N  N  45  
VDA  C9   H9A   SING  N  N  46  
VDA  C10  H10   SING  N  N  47  
VDA  C10  H10A  SING  N  N  48  
VDA  C11  H11   SING  N  N  49  
VDA  C11  H11A  SING  N  N  50  
VDA  C12  H12   SING  N  N  51  
VDA  C12  H12A  SING  N  N  52  
VDA  C14  H14   SING  N  N  53  
VDA  C15  H15   SING  N  N  54  
VDA  C15  H15A  SING  N  N  55  
VDA  C16  H16   SING  N  N  56  
VDA  C18  H18   SING  N  N  57  
VDA  C18  H18A  SING  N  N  58  
VDA  C18  H18B  SING  N  N  59  
VDA  C20  H20   SING  N  N  60  
VDA  C21  H21   SING  N  N  61  
VDA  C21  H21A  SING  N  N  62  
VDA  C21  H21B  SING  N  N  63  
VDA  C23  H23   SING  N  N  64  
VDA  C23  H23A  SING  N  N  65  
VDA  O3   HO3   SING  N  N  66  
VDA  C26  H26   SING  N  N  67  
VDA  C26  H26A  SING  N  N  68  
VDA  C27  H27   SING  N  N  69  
VDA  C27  H27A  SING  N  N  70  
VDA  O1   HO1   SING  N  N  71  
VDA  C30  H30   SING  N  N  72  
VDA  C30  H30A  SING  N  N  73  
VDA  C31  H31   SING  N  N  74  
VDA  C31  H31A  SING  N  N  75  
VDA  O5   HO5   SING  N  N  76  
VDA  C29  H29   SING  N  N  77  
VDA  C29  H29A  SING  N  N  78  
VDA  C29  H29B  SING  N  N  79  
VDA  C28  H28   SING  N  N  80  
VDA  C28  H28A  SING  N  N  81  
VDA  C28  H28B  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
VDA  SMILES            ACDLabs               10.04  "O(CCO)C3C(O)C/C(=C/C=C1\CCCC2(C(=CCC12)C(SCC(O)(CC)CC)C)C)CC3O"  
VDA  SMILES_CANONICAL  CACTVS                3.341  "CCC(O)(CC)CS[C@@H](C)C1=CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)[C@@H](OCCO)[C@H](O)C3"  
VDA  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"  
VDA  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CCC(CC)(CS[C@@H](C)C1=CC[C@@H]2[C@@]1(CCCC2=CC=C3C[C@H](C([C@@H](C3)O)OCCO)O)C)O"  
VDA  SMILES            "OpenEye OEToolkits"  1.5.0  "CCC(CC)(CSC(C)C1=CCC2C1(CCCC2=CC=C3CC(C(C(C3)O)OCCO)O)C)O"  
VDA  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+/m0/s1"  
VDA  InChIKey          InChI                 1.03   DUIYWCMQVXJTIP-YYDWSLPPSA-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
VDA  "SYSTEMATIC NAME"  ACDLabs               10.04  "(1R,2S,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol"  
VDA  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(1R,3R)-5-[2-[(3aS,7aS)-1-[(1S)-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
VDA  "Create component"   2008-04-09  PDBJ  
VDA  "Modify descriptor"  2011-06-04  RCSB  
VDA  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     VDA
_pdbx_chem_comp_synonyms.name        "(20S)-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        ?
##
