data_1Y9 # _chem_comp.id 1Y9 _chem_comp.name "vibralactone, bound form" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H18 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(1R,5S)-5-hydroxy-3-(hydroxymethyl)-1-(3-methylbut-2-en-1-yl)cyclopent-2-ene-1-carbaldehyde" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-08-01 _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 210.270 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1Y9 _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 4LQI _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 1Y9 O1 O1 O 0 1 N N N 11.482 -140.981 12.404 1.488 2.487 0.140 O1 1Y9 1 1Y9 C2 C2 C 0 1 N N S 11.210 -139.881 13.317 0.999 1.499 -0.770 C2 1Y9 2 1Y9 C3 C3 C 0 1 N N R 12.134 -138.623 13.050 0.091 0.479 -0.046 C3 1Y9 3 1Y9 C4 C4 C 0 1 N N N 12.930 -138.739 11.758 -0.522 1.100 1.183 C4 1Y9 4 1Y9 O5 O5 O 0 1 N N N 13.879 -137.703 11.421 -0.269 2.245 1.470 O5 1Y9 5 1Y9 C6 C6 C 0 1 N N N 11.365 -137.274 12.878 -1.002 -0.026 -0.991 C6 1Y9 6 1Y9 C7 C7 C 0 1 N N N 10.428 -136.821 13.953 -1.874 -1.018 -0.266 C7 1Y9 7 1Y9 C8 C8 C 0 1 N N N 9.839 -135.607 14.040 -3.163 -0.806 -0.165 C8 1Y9 8 1Y9 C9 C9 C 0 1 N N N 10.043 -134.455 13.031 -4.055 -1.857 0.443 C9 1Y9 9 1Y9 C10 C10 C 0 1 N N N 8.907 -135.322 15.181 -3.754 0.490 -0.658 C10 1Y9 10 1Y9 C11 C11 C 0 1 N N N 13.102 -138.678 14.192 1.015 -0.652 0.341 C11 1Y9 11 1Y9 C12 C12 C 0 1 N N N 12.758 -139.599 15.097 2.136 -0.592 -0.326 C12 1Y9 12 1Y9 C13 C13 C 0 1 N N N 13.468 -139.976 16.369 3.271 -1.572 -0.176 C13 1Y9 13 1Y9 O14 O14 O 0 1 N N N 14.035 -138.832 17.010 2.923 -2.558 0.799 O14 1Y9 14 1Y9 C15 C15 C 0 1 N N N 11.485 -140.338 14.770 2.145 0.589 -1.269 C15 1Y9 15 1Y9 H1 H1 H 0 1 N N N 10.905 -141.709 12.604 2.140 3.088 -0.245 H1 1Y9 16 1Y9 H2 H2 H 0 1 N N N 10.159 -139.567 13.233 0.478 1.965 -1.606 H2 1Y9 17 1Y9 H3 H3 H 0 1 N N N 12.787 -139.585 11.102 -1.186 0.521 1.806 H3 1Y9 18 1Y9 H6 H6 H 0 1 N N N 12.123 -136.486 12.760 -1.609 0.815 -1.326 H6 1Y9 19 1Y9 H7 H7 H 0 1 N N N 10.776 -137.357 11.953 -0.542 -0.508 -1.853 H7 1Y9 20 1Y9 H8 H8 H 0 1 N N N 10.200 -137.531 14.734 -1.437 -1.903 0.171 H8 1Y9 21 1Y9 H9 H9 H 0 1 N N N 9.447 -133.585 13.342 -3.453 -2.717 0.739 H9 1Y9 22 1Y9 H10 H10 H 0 1 N N N 11.107 -134.178 13.001 -4.556 -1.446 1.320 H10 1Y9 23 1Y9 H11 H11 H 0 1 N N N 9.720 -134.782 12.031 -4.800 -2.170 -0.288 H11 1Y9 24 1Y9 H12 H12 H 0 1 N N N 8.840 -136.208 15.830 -3.953 0.415 -1.728 H12 1Y9 25 1Y9 H13 H13 H 0 1 N N N 9.289 -134.470 15.762 -4.687 0.688 -0.129 H13 1Y9 26 1Y9 H14 H14 H 0 1 N N N 7.909 -135.079 14.787 -3.052 1.303 -0.475 H14 1Y9 27 1Y9 H15 H15 H 0 1 N N N 13.975 -138.048 14.274 0.780 -1.410 1.073 H15 1Y9 28 1Y9 H18 H18 H 0 1 N N N 12.749 -140.449 17.053 3.460 -2.058 -1.133 H18 1Y9 29 1Y9 H19 H19 H 0 1 N N N 14.272 -140.688 16.132 4.168 -1.043 0.147 H19 1Y9 30 1Y9 H20 H20 H 0 1 N N N 14.475 -139.101 17.808 3.609 -3.223 0.948 H20 1Y9 31 1Y9 H21 H21 H 0 1 N N N 10.667 -140.042 15.443 1.952 0.261 -2.290 H21 1Y9 32 1Y9 H22 H22 H 0 1 N N N 11.630 -141.427 14.826 3.099 1.113 -1.211 H22 1Y9 33 # # 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 1Y9 O5 C4 DOUB N N 1 1Y9 C4 C3 SING N N 2 1Y9 O1 C2 SING N N 3 1Y9 C6 C3 SING N N 4 1Y9 C6 C7 SING N N 5 1Y9 C9 C8 SING N N 6 1Y9 C3 C2 SING N N 7 1Y9 C3 C11 SING N N 8 1Y9 C2 C15 SING N N 9 1Y9 C7 C8 DOUB N N 10 1Y9 C8 C10 SING N N 11 1Y9 C11 C12 DOUB N N 12 1Y9 C15 C12 SING N N 13 1Y9 C12 C13 SING N N 14 1Y9 C13 O14 SING N N 15 1Y9 O1 H1 SING N N 16 1Y9 C2 H2 SING N N 17 1Y9 C4 H3 SING N N 18 1Y9 C6 H6 SING N N 19 1Y9 C6 H7 SING N N 20 1Y9 C7 H8 SING N N 21 1Y9 C9 H9 SING N N 22 1Y9 C9 H10 SING N N 23 1Y9 C9 H11 SING N N 24 1Y9 C10 H12 SING N N 25 1Y9 C10 H13 SING N N 26 1Y9 C10 H14 SING N N 27 1Y9 C11 H15 SING N N 28 1Y9 C13 H18 SING N N 29 1Y9 C13 H19 SING N N 30 1Y9 O14 H20 SING N N 31 1Y9 C15 H21 SING N N 32 1Y9 C15 H22 SING N N 33 # # 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 1Y9 SMILES ACDLabs 12.01 "O=CC1(C=C(CC1O)CO)C\C=C(/C)C" 1Y9 InChI InChI 1.03 "InChI=1S/C12H18O3/c1-9(2)3-4-12(8-14)6-10(7-13)5-11(12)15/h3,6,8,11,13,15H,4-5,7H2,1-2H3/t11-,12-/m0/s1" 1Y9 InChIKey InChI 1.03 WFKBKCXWCUVGHP-RYUDHWBXSA-N 1Y9 SMILES_CANONICAL CACTVS 3.385 "CC(C)=CC[C@@]1(C=O)C=C(CO)C[C@@H]1O" 1Y9 SMILES CACTVS 3.385 "CC(C)=CC[C]1(C=O)C=C(CO)C[CH]1O" 1Y9 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(=CC[C@]1(C=C(C[C@@H]1O)CO)C=O)C" 1Y9 SMILES "OpenEye OEToolkits" 1.7.6 "CC(=CCC1(C=C(CC1O)CO)C=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 1Y9 "SYSTEMATIC NAME" ACDLabs 12.01 "(1R,5S)-5-hydroxy-3-(hydroxymethyl)-1-(3-methylbut-2-en-1-yl)cyclopent-2-ene-1-carbaldehyde" 1Y9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(1R,5S)-3-(hydroxymethyl)-1-(3-methylbut-2-enyl)-5-oxidanyl-cyclopent-2-ene-1-carbaldehyde" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 1Y9 "Create component" 2013-08-01 RCSB 1Y9 "Other modification" 2013-08-02 RCSB 1Y9 "Initial release" 2013-12-25 RCSB 1Y9 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 1Y9 _pdbx_chem_comp_synonyms.name "(1R,5S)-5-hydroxy-3-(hydroxymethyl)-1-(3-methylbut-2-en-1-yl)cyclopent-2-ene-1-carbaldehyde" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##