data_YSV
#

_chem_comp.id                                   YSV
_chem_comp.name                                 
;(1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2-
methylenecyclohexane-1,3-diol
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C27 H44 O3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2-methylidene-19-nor-1alpha,25-dihydroxyvitamin D3"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-03-30
_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                       416.636
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YSV
_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       5B41
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
YSV  O3   O1   O  0  1  N  N  N   9.144  -1.571  28.319  -8.097   0.557   1.300  O3   YSV   1  
YSV  C25  C1   C  0  1  N  N  N   8.605  -0.597  27.430  -7.656   1.602   0.430  C25  YSV   2  
YSV  C27  C2   C  0  1  N  N  N   7.853   0.446  28.254  -8.855   2.177  -0.326  C27  YSV   3  
YSV  C26  C3   C  0  1  N  N  N   7.639  -1.310  26.476  -6.995   2.708   1.256  C26  YSV   4  
YSV  C24  C4   C  0  1  N  N  N   9.772   0.021  26.650  -6.644   1.040  -0.571  C24  YSV   5  
YSV  C23  C5   C  0  1  N  N  N  10.654   0.914  27.539  -5.445   0.465   0.185  C23  YSV   6  
YSV  C22  C6   C  0  1  N  N  N  11.855   1.459  26.753  -4.433  -0.098  -0.816  C22  YSV   7  
YSV  C20  C7   C  0  1  N  N  R  12.757   2.279  27.657  -3.234  -0.673  -0.060  C20  YSV   8  
YSV  C21  C8   C  0  1  N  N  N  13.334   1.414  28.751  -3.685  -1.872   0.776  C21  YSV   9  
YSV  C17  C9   C  0  1  N  N  R  13.894   3.029  26.919  -2.168  -1.122  -1.062  C17  YSV  10  
YSV  C16  C10  C  0  1  N  N  N  14.564   2.298  25.742  -1.645   0.093  -1.872  C16  YSV  11  
YSV  C13  C11  C  0  1  N  N  R  13.530   4.399  26.389  -0.951  -1.665  -0.330  C13  YSV  12  
YSV  C18  C12  C  0  1  N  N  N  12.271   4.331  25.495  -0.763  -0.894   0.979  C18  YSV  13  
YSV  C14  C13  C  0  1  N  N  S  14.776   4.690  25.539   0.225  -1.315  -1.286  C14  YSV  14  
YSV  C15  C14  C  0  1  N  N  N  15.105   3.374  24.780  -0.107   0.138  -1.648  C15  YSV  15  
YSV  C12  C15  C  0  1  N  N  N  13.378   5.498  27.398  -0.885  -3.148  -0.049  C12  YSV  16  
YSV  C11  C16  C  0  1  N  N  N  13.123   6.872  26.674   0.379  -3.406   0.788  C11  YSV  17  
YSV  C9   C17  C  0  1  N  N  N  14.226   7.176  25.630   1.643  -2.954   0.061  C9   YSV  18  
YSV  C8   C18  C  0  1  N  N  N  14.576   5.963  24.776   1.474  -1.556  -0.491  C8   YSV  19  
YSV  C7   C19  C  0  1  N  N  N  14.714   6.028  23.436   2.374  -0.603  -0.274  C7   YSV  20  
YSV  C6   C20  C  0  1  N  N  N  14.488   7.291  22.716   3.647  -0.930   0.387  C6   YSV  21  
YSV  C5   C21  C  0  1  N  N  N  14.276   7.354  21.382   4.500   0.038   0.702  C5   YSV  22  
YSV  C10  C22  C  0  1  N  N  N  14.039   8.715  20.771   5.740  -0.262   1.514  C10  YSV  23  
YSV  C4   C23  C  0  1  N  N  N  14.208   6.105  20.542   4.252   1.459   0.250  C4   YSV  24  
YSV  C3   C24  C  0  1  N  N  R  14.701   6.267  19.108   5.482   1.947  -0.526  C3   YSV  25  
YSV  O2   O2   O  0  1  N  N  N  14.220   5.235  18.249   5.381   3.355  -0.750  O2   YSV  26  
YSV  C2   C25  C  0  1  N  N  N  14.330   7.606  18.558   6.718   1.648   0.291  C2   YSV  27  
YSV  C28  C26  C  0  1  N  N  N  13.743   7.758  17.385   7.560   2.603   0.602  C28  YSV  28  
YSV  C1   C27  C  0  1  N  N  R  14.710   8.817  19.393   6.966   0.230   0.735  C1   YSV  29  
YSV  O1   O3   O  0  1  N  N  N  16.119   8.829  19.512   7.180  -0.601  -0.408  O1   YSV  30  
YSV  H1   H1   H  0  1  N  N  N   9.747  -1.151  28.921  -8.526  -0.179   0.843  H1   YSV  31  
YSV  H2   H2   H  0  1  N  N  N   8.554   0.951  28.935  -9.576   2.578   0.388  H2   YSV  32  
YSV  H3   H3   H  0  1  N  N  N   7.398   1.187  27.580  -8.519   2.974  -0.989  H3   YSV  33  
YSV  H4   H4   H  0  1  N  N  N   7.065  -0.049  28.841  -9.326   1.390  -0.914  H4   YSV  34  
YSV  H5   H5   H  0  1  N  N  N   6.810  -1.747  27.052  -7.716   3.109   1.969  H5   YSV  35  
YSV  H6   H6   H  0  1  N  N  N   7.240  -0.586  25.750  -6.141   2.298   1.794  H6   YSV  36  
YSV  H7   H7   H  0  1  N  N  N   8.174  -2.109  25.942  -6.659   3.505   0.593  H7   YSV  37  
YSV  H8   H8   H  0  1  N  N  N  10.391  -0.789  26.236  -7.115   0.252  -1.159  H8   YSV  38  
YSV  H9   H9   H  0  1  N  N  N   9.367   0.629  25.828  -6.308   1.837  -1.234  H9   YSV  39  
YSV  H10  H10  H  0  1  N  N  N  10.053   1.758  27.909  -4.974   1.253   0.773  H10  YSV  40  
YSV  H11  H11  H  0  1  N  N  N  11.020   0.323  28.391  -5.781  -0.332   0.848  H11  YSV  41  
YSV  H12  H12  H  0  1  N  N  N  12.428   0.617  26.338  -4.904  -0.885  -1.404  H12  YSV  42  
YSV  H13  H13  H  0  1  N  N  N  11.492   2.095  25.932  -4.097   0.699  -1.479  H13  YSV  43  
YSV  H14  H14  H  0  1  N  N  N  12.129   3.043  28.139  -2.817   0.091   0.595  H14  YSV  44  
YSV  H15  H15  H  0  1  N  N  N  13.984   2.023  29.396  -2.830  -2.282   1.314  H15  YSV  45  
YSV  H16  H16  H  0  1  N  N  N  12.516   0.989  29.352  -4.445  -1.552   1.489  H16  YSV  46  
YSV  H17  H17  H  0  1  N  N  N  13.922   0.599  28.303  -4.102  -2.636   0.120  H17  YSV  47  
YSV  H18  H18  H  0  1  N  N  N  14.685   3.188  27.667  -2.575  -1.878  -1.733  H18  YSV  48  
YSV  H19  H19  H  0  1  N  N  N  13.828   1.666  25.224  -1.864  -0.041  -2.932  H19  YSV  49  
YSV  H20  H20  H  0  1  N  N  N  15.391   1.672  26.109  -2.104   1.012  -1.509  H20  YSV  50  
YSV  H21  H21  H  0  1  N  N  N  11.389   4.122  26.118  -1.568  -1.148   1.668  H21  YSV  51  
YSV  H22  H22  H  0  1  N  N  N  12.136   5.293  24.979   0.195  -1.163   1.424  H22  YSV  52  
YSV  H23  H23  H  0  1  N  N  N  12.392   3.530  24.751  -0.782   0.176   0.775  H23  YSV  53  
YSV  H24  H24  H  0  1  N  N  N  15.605   4.860  26.242   0.205  -1.946  -2.174  H24  YSV  54  
YSV  H25  H25  H  0  1  N  N  N  14.591   3.335  23.808   0.410   0.436  -2.560  H25  YSV  55  
YSV  H26  H26  H  0  1  N  N  N  16.188   3.263  24.626   0.143   0.808  -0.825  H26  YSV  56  
YSV  H27  H27  H  0  1  N  N  N  12.526   5.271  28.056  -1.768  -3.459   0.508  H27  YSV  57  
YSV  H28  H28  H  0  1  N  N  N  14.297   5.569  27.998  -0.827  -3.700  -0.988  H28  YSV  58  
YSV  H29  H29  H  0  1  N  N  N  13.111   7.675  27.425   0.297  -2.864   1.730  H29  YSV  59  
YSV  H30  H30  H  0  1  N  N  N  12.149   6.832  26.164   0.454  -4.473   0.998  H30  YSV  60  
YSV  H31  H31  H  0  1  N  N  N  15.131   7.506  26.160   2.483  -2.970   0.756  H31  YSV  61  
YSV  H32  H32  H  0  1  N  N  N  13.873   7.982  24.969   1.847  -3.637  -0.764  H32  YSV  62  
YSV  H33  H33  H  0  1  N  N  N  14.994   5.142  22.885   2.171   0.412  -0.582  H33  YSV  63  
YSV  H34  H34  H  0  1  N  N  N  14.492   8.212  23.280   3.888  -1.958   0.616  H34  YSV  64  
YSV  H35  H35  H  0  1  N  N  N  14.458   9.486  21.434   5.683   0.254   2.472  H35  YSV  65  
YSV  H36  H36  H  0  1  N  N  N  12.957   8.876  20.658   5.816  -1.337   1.681  H36  YSV  66  
YSV  H37  H37  H  0  1  N  N  N  13.160   5.773  20.507   3.376   1.490  -0.398  H37  YSV  67  
YSV  H38  H38  H  0  1  N  N  N  14.821   5.332  21.029   4.088   2.096   1.119  H38  YSV  68  
YSV  H39  H39  H  0  1  N  N  N  15.799   6.213  19.134   5.542   1.428  -1.483  H39  YSV  69  
YSV  H40  H40  H  0  1  N  N  N  14.460   4.388  18.606   6.127   3.731  -1.237  H40  YSV  70  
YSV  H41  H41  H  0  1  N  N  N  13.529   8.749  17.012   7.373   3.615   0.274  H41  YSV  71  
YSV  H42  H42  H  0  1  N  N  N  13.476   6.891  16.798   8.440   2.378   1.186  H42  YSV  72  
YSV  H43  H43  H  0  1  N  N  N  14.355   9.728  18.890   7.844   0.196   1.381  H43  YSV  73  
YSV  H44  H44  H  0  1  N  N  N  16.387   9.578  20.031   7.936  -0.337  -0.950  H44  YSV  74  
#   #
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
YSV  C28  C2   DOUB  N  N   1  
YSV  O2   C3   SING  N  N   2  
YSV  C2   C3   SING  N  N   3  
YSV  C2   C1   SING  N  N   4  
YSV  C3   C4   SING  N  N   5  
YSV  C1   O1   SING  N  N   6  
YSV  C1   C10  SING  N  N   7  
YSV  C4   C5   SING  N  N   8  
YSV  C10  C5   SING  N  N   9  
YSV  C5   C6   DOUB  N  N  10  
YSV  C6   C7   SING  N  N  11  
YSV  C7   C8   DOUB  N  E  12  
YSV  C8   C14  SING  N  N  13  
YSV  C8   C9   SING  N  N  14  
YSV  C15  C14  SING  N  N  15  
YSV  C15  C16  SING  N  N  16  
YSV  C18  C13  SING  N  N  17  
YSV  C14  C13  SING  N  N  18  
YSV  C9   C11  SING  N  N  19  
YSV  C16  C17  SING  N  N  20  
YSV  C13  C17  SING  N  N  21  
YSV  C13  C12  SING  N  N  22  
YSV  C26  C25  SING  N  N  23  
YSV  C24  C25  SING  N  N  24  
YSV  C24  C23  SING  N  N  25  
YSV  C11  C12  SING  N  N  26  
YSV  C22  C23  SING  N  N  27  
YSV  C22  C20  SING  N  N  28  
YSV  C17  C20  SING  N  N  29  
YSV  C25  C27  SING  N  N  30  
YSV  C25  O3   SING  N  N  31  
YSV  C20  C21  SING  N  N  32  
YSV  O3   H1   SING  N  N  33  
YSV  C27  H2   SING  N  N  34  
YSV  C27  H3   SING  N  N  35  
YSV  C27  H4   SING  N  N  36  
YSV  C26  H5   SING  N  N  37  
YSV  C26  H6   SING  N  N  38  
YSV  C26  H7   SING  N  N  39  
YSV  C24  H8   SING  N  N  40  
YSV  C24  H9   SING  N  N  41  
YSV  C23  H10  SING  N  N  42  
YSV  C23  H11  SING  N  N  43  
YSV  C22  H12  SING  N  N  44  
YSV  C22  H13  SING  N  N  45  
YSV  C20  H14  SING  N  N  46  
YSV  C21  H15  SING  N  N  47  
YSV  C21  H16  SING  N  N  48  
YSV  C21  H17  SING  N  N  49  
YSV  C17  H18  SING  N  N  50  
YSV  C16  H19  SING  N  N  51  
YSV  C16  H20  SING  N  N  52  
YSV  C18  H21  SING  N  N  53  
YSV  C18  H22  SING  N  N  54  
YSV  C18  H23  SING  N  N  55  
YSV  C14  H24  SING  N  N  56  
YSV  C15  H25  SING  N  N  57  
YSV  C15  H26  SING  N  N  58  
YSV  C12  H27  SING  N  N  59  
YSV  C12  H28  SING  N  N  60  
YSV  C11  H29  SING  N  N  61  
YSV  C11  H30  SING  N  N  62  
YSV  C9   H31  SING  N  N  63  
YSV  C9   H32  SING  N  N  64  
YSV  C7   H33  SING  N  N  65  
YSV  C6   H34  SING  N  N  66  
YSV  C10  H35  SING  N  N  67  
YSV  C10  H36  SING  N  N  68  
YSV  C4   H37  SING  N  N  69  
YSV  C4   H38  SING  N  N  70  
YSV  C3   H39  SING  N  N  71  
YSV  O2   H40  SING  N  N  72  
YSV  C28  H41  SING  N  N  73  
YSV  C28  H42  SING  N  N  74  
YSV  C1   H43  SING  N  N  75  
YSV  O1   H44  SING  N  N  76  
#   #
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
YSV  SMILES            ACDLabs               12.01  "OC(C)(C)CCCC(C)C1CCC2C1(CCCC2=[C@H][C@H]=C3CC(C(\C(C3)O)=C)O)C"  
YSV  InChI             InChI                 1.03   "InChI=1S/C27H44O3/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/h10-11,18,22-25,28-30H,2,6-9,12-17H2,1,3-5H3/b21-11+/t18-,22-,23+,24-,25-,27-/m1/s1"  
YSV  InChIKey          InChI                 1.03   UHMPCVGLSKFXHR-JUTHDLPNSA-N  
YSV  SMILES_CANONICAL  CACTVS                3.385  "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(=C)[C@H](O)C/3"  
YSV  SMILES            CACTVS                3.385  "C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3"  
YSV  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.4  "C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C"  
YSV  SMILES            "OpenEye OEToolkits"  2.0.4  "CC(CCCC(C)(C)O)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
YSV  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1R,3R,7E,17beta)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol"  
YSV  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.4  "(1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-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
YSV  "Create component"               2016-03-30  PDBJ  
YSV  "Modify model coordinates code"  2016-06-07  PDBJ  
YSV  "Initial release"                2016-12-07  RCSB  
YSV  "Modify synonyms"                2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     YSV
_pdbx_chem_comp_synonyms.name        "2-methylidene-19-nor-1alpha,25-dihydroxyvitamin D3"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
