data_PPY
#
_chem_comp.id PPY
_chem_comp.name "3-PHENYLPYRUVIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H8 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces 1PY
_chem_comp.formula_weight 164.158
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PPY
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1LCO
_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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
PPY C1 C1 C 0 1 N N N N N N 67.421 54.297 5.381 -0.051 -0.000 2.793 C1 PPY 1
PPY O1 O1 O 0 1 N N N N N N 66.441 54.923 4.909 -1.179 -0.011 3.238 O1 PPY 2
PPY O2 O2 O 0 1 N N N N N N 68.567 54.591 4.964 1.002 0.010 3.630 O2 PPY 3
PPY C2 C2 C 0 1 N N N N N N 67.247 53.094 6.134 0.168 0.001 1.318 C2 PPY 4
PPY O3 O3 O 0 1 N N N N N N 66.081 52.645 6.261 1.292 0.013 0.875 O3 PPY 5
PPY C3 C3 C 0 1 N N N N N N 68.291 52.677 7.195 -1.011 -0.010 0.381 C3 PPY 6
PPY "C1'" "C1'" C 0 1 Y N N N N N 68.032 51.211 7.482 -0.520 -0.005 -1.043 "C1'" PPY 7
PPY "C2'" "C2'" C 0 1 Y N N N N N 68.698 50.242 6.743 -0.283 -1.200 -1.697 "C2'" PPY 8
PPY "C3'" "C3'" C 0 1 Y N N N N N 68.414 48.905 6.939 0.166 -1.195 -3.004 "C3'" PPY 9
PPY "C4'" "C4'" C 0 1 Y N N N N N 67.473 48.548 7.873 0.379 0.003 -3.657 "C4'" PPY 10
PPY "C5'" "C5'" C 0 1 Y N N N N N 66.817 49.518 8.610 0.141 1.198 -3.004 "C5'" PPY 11
PPY "C6'" "C6'" C 0 1 Y N N N N N 67.089 50.851 8.425 -0.313 1.193 -1.699 "C6'" PPY 12
PPY HO2 HO2 H 0 1 N N N N N N 69.308 54.117 5.321 0.860 0.009 4.586 HO2 PPY 13
PPY H31 1H3 H 0 1 N N N N N N 69.342 52.892 6.893 -1.606 -0.906 0.557 H31 PPY 14
PPY H32 2H3 H 0 1 N N N N N N 68.278 53.317 8.107 -1.624 0.873 0.557 H32 PPY 15
PPY "H2'" "H2'" H 0 1 N N N N N N 69.455 50.535 5.997 -0.449 -2.137 -1.186 "H2'" PPY 16
PPY "H3'" "H3'" H 0 1 N N N N N N 68.934 48.128 6.354 0.352 -2.129 -3.514 "H3'" PPY 17
PPY "H4'" "H4'" H 0 1 N N N N N N 67.243 47.480 8.031 0.731 0.007 -4.678 "H4'" PPY 18
PPY "H5'" "H5'" H 0 1 N N N N N N 66.063 49.223 9.359 0.307 2.135 -3.515 "H5'" PPY 19
PPY "H6'" "H6'" H 0 1 N N N N N N 66.561 51.615 9.020 -0.499 2.127 -1.188 "H6'" PPY 20
#
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
PPY C1 O1 DOUB N N 1
PPY C1 O2 SING N N 2
PPY C1 C2 SING N N 3
PPY O2 HO2 SING N N 4
PPY C2 O3 DOUB N N 5
PPY C2 C3 SING N N 6
PPY C3 "C1'" SING N N 7
PPY C3 H31 SING N N 8
PPY C3 H32 SING N N 9
PPY "C1'" "C2'" DOUB Y N 10
PPY "C1'" "C6'" SING Y N 11
PPY "C2'" "C3'" SING Y N 12
PPY "C2'" "H2'" SING N N 13
PPY "C3'" "C4'" DOUB Y N 14
PPY "C3'" "H3'" SING N N 15
PPY "C4'" "C5'" SING Y N 16
PPY "C4'" "H4'" SING N N 17
PPY "C5'" "C6'" DOUB Y N 18
PPY "C5'" "H5'" SING N N 19
PPY "C6'" "H6'" SING N N 20
#
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
PPY SMILES ACDLabs 10.04 O=C(C(=O)O)Cc1ccccc1
PPY SMILES_CANONICAL CACTVS 3.341 OC(=O)C(=O)Cc1ccccc1
PPY SMILES CACTVS 3.341 OC(=O)C(=O)Cc1ccccc1
PPY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)CC(=O)C(=O)O
PPY SMILES "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)CC(=O)C(=O)O
PPY InChI InChI 1.03 InChI=1S/C9H8O3/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5H,6H2,(H,11,12)
PPY InChIKey InChI 1.03 BTNMPGBKDVTSJY-UHFFFAOYSA-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
PPY "SYSTEMATIC NAME" ACDLabs 10.04 "2-oxo-3-phenylpropanoic acid"
PPY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "2-oxo-3-phenyl-propanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PPY 'Create component' 1999-07-08 RCSB
PPY 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id PPY
_pdbe_chem_comp_drugbank_details.drugbank_id DB03884
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Phenylpyruvic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 156-06-9
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
PPY '2-oxo-3-phenylpropanic acid' DrugBank ?
PPY 3-phenyl-2-oxopropanoate DrugBank ?
PPY '3-phenyl-2-oxopropanoic acid' DrugBank ?
PPY '3-phenylpyruvic acid' DrugBank ?
PPY 'alpha-Ketohydrocinnamic acid' DrugBank ?
PPY keto-Phenylpyruvate DrugBank ?
PPY 'keto-phenylpyruvic acid' DrugBank ?
PPY Phenylpyruvate DrugBank ?
PPY 'Phenylpyruvic acid' DrugBank ?
PPY 'α-oxo-benzenepropanoic acid' DrugBank ?
PPY 'β-phenylpyruvic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id PPY
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03884
_pdbe_chem_comp_drugbank_classification.parent 'Phenylpyruvic acid derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Benzene and substituted derivatives'
_pdbe_chem_comp_drugbank_classification.superclass Benzenoids
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as phenylpyruvic acid derivatives. These are compounds containing a phenylpyruvic acid moiety, which consists of a phenyl group substituted at the second position by an pyruvic acid.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
PPY DB03884 'Phenylalanine dehydrogenase' 'Rhodococcus sp.' Q59771 unknown 1
PPY DB03884 '2-Hydroxyacid oxidase 1' Humans Q9UJM8 unknown 2
PPY DB03884 'Indole-3-pyruvate decarboxylase' 'Azospirillum brasilense' P51852 unknown 3
PPY DB03884 'Putative uncharacterized protein' 'Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757)' Q7NSZ5 unknown 4
PPY DB03884 'Bacilysin biosynthesis protein BacB' 'Bacillus subtilis (strain 168)' P39639 unknown 5
PPY DB03884 'Probable chorismate mutase' 'Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)' A1A2B5 unknown 6
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
PPY C1 C 5.598 2.535 1
PPY O1 O 6.897 3.285 2
PPY O2 O 4.299 3.285 3
PPY C2 C 5.598 1.035 4
PPY O3 O 6.897 0.285 5
PPY C3 C 4.299 0.285 6
PPY "C1'" C 4.299 -1.215 7
PPY "C2'" C 3.000 -1.965 8
PPY "C3'" C 3.000 -3.465 9
PPY "C4'" C 4.299 -4.215 10
PPY "C5'" C 5.598 -3.465 11
PPY "C6'" C 5.598 -1.965 12
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
PPY C1 O1 DOUBLE NONE 1
PPY C1 O2 SINGLE NONE 2
PPY C1 C2 SINGLE NONE 3
PPY C2 O3 DOUBLE NONE 4
PPY C2 C3 SINGLE NONE 5
PPY C3 "C1'" SINGLE NONE 6
PPY "C1'" "C2'" DOUBLE NONE 7
PPY "C1'" "C6'" SINGLE NONE 8
PPY "C2'" "C3'" SINGLE NONE 9
PPY "C3'" "C4'" DOUBLE NONE 10
PPY "C4'" "C5'" SINGLE NONE 11
PPY "C5'" "C6'" DOUBLE NONE 12
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
PPY MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
PPY phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
PPY "C1'" S1 1
PPY "C2'" S1 1
PPY "C3'" S1 1
PPY "C4'" S1 1
PPY "C5'" S1 1
PPY "C6'" S1 1
PPY "C1'" F1 1
PPY "C2'" F1 1
PPY "C3'" F1 1
PPY "C4'" F1 1
PPY "C5'" F1 1
PPY "C6'" F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PPY
_pdbe_chem_comp_rdkit_properties.exactmw 164.047
_pdbe_chem_comp_rdkit_properties.amw 164.160
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 20
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.111
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 80.970
_pdbe_chem_comp_rdkit_properties.tpsa 54.370
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.828
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.523
_pdbe_chem_comp_rdkit_properties.chi0v 5.725
_pdbe_chem_comp_rdkit_properties.chi1v 2.862
_pdbe_chem_comp_rdkit_properties.chi2v 0.924
_pdbe_chem_comp_rdkit_properties.chi3v 0.924
_pdbe_chem_comp_rdkit_properties.chi4v 0.477
_pdbe_chem_comp_rdkit_properties.chi0n 13.725
_pdbe_chem_comp_rdkit_properties.chi1n 6.771
_pdbe_chem_comp_rdkit_properties.chi2n 0.924
_pdbe_chem_comp_rdkit_properties.chi3n 0.924
_pdbe_chem_comp_rdkit_properties.chi4n 0.477
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.640
_pdbe_chem_comp_rdkit_properties.kappa1 2.693
_pdbe_chem_comp_rdkit_properties.kappa2 3.665
_pdbe_chem_comp_rdkit_properties.kappa3 2.196
_pdbe_chem_comp_rdkit_properties.Phi 0.822
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
PPY UniChem DrugBank DB03884
PPY UniChem 'KEGG LIGAND' C00166
PPY UniChem ChEBI 30851
PPY UniChem ZINC ZINC000000901485
PPY UniChem eMolecules 494845
PPY UniChem fdasrs X7CO62M413
PPY UniChem SureChEMBL SCHEMBL43235
PPY UniChem HMDB HMDB0000205
PPY UniChem NMRShiftDB 60020657
PPY UniChem Nikkaji J11.025F
PPY UniChem 'EPA CompTox Dashboard' DTXSID1042281
PPY UniChem MetaboLights MTBLC30851
PPY UniChem BRENDA 10866
PPY UniChem BRENDA 12773
PPY UniChem BRENDA 198
PPY UniChem BRENDA 29410
PPY UniChem BRENDA 29509
PPY UniChem BRENDA 32519
PPY UniChem BRENDA 4914
PPY UniChem BRENDA 8175
PPY UniChem BRENDA 91537
PPY UniChem MedChemExpress HY-W012530
PPY UniChem 'Probes And Drugs' PD007156
PPY UniChem ChemicalBook CB1761595
PPY UniChem 'PubChem TPHARMA' 15194921
PPY UniChem PubChem 997
PPY UniChem Mcule MCULE-9935480822
PPY UniChem ACTor 156-06-9
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
PPY C1 2.741 0.439 -0.063 ETKDGv3 1
PPY O1 2.553 0.419 -1.309 ETKDGv3 2
PPY O2 3.696 1.295 0.477 ETKDGv3 3
PPY C2 1.959 -0.436 0.825 ETKDGv3 4
PPY O3 2.156 -0.387 2.069 ETKDGv3 5
PPY C3 0.900 -1.355 0.287 ETKDGv3 6
PPY "C1'" -0.414 -0.631 0.182 ETKDGv3 7
PPY "C2'" -0.805 -0.072 -0.978 ETKDGv3 8
PPY "C3'" -2.084 0.664 -1.056 ETKDGv3 9
PPY "C4'" -2.855 0.787 0.031 ETKDGv3 10
PPY "C5'" -2.427 0.188 1.312 ETKDGv3 11
PPY "C6'" -1.271 -0.482 1.386 ETKDGv3 12
PPY HO2 4.243 1.905 -0.118 ETKDGv3 13
PPY H31 1.210 -1.763 -0.700 ETKDGv3 14
PPY H32 0.787 -2.228 0.967 ETKDGv3 15
PPY "H2'" -0.191 -0.152 -1.866 ETKDGv3 16
PPY "H3'" -2.395 1.104 -1.994 ETKDGv3 17
PPY "H4'" -3.792 1.327 -0.024 ETKDGv3 18
PPY "H5'" -3.051 0.295 2.190 ETKDGv3 19
PPY "H6'" -0.961 -0.915 2.329 ETKDGv3 20
#