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        ?
##
