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 ? ##