data_PYR
#
_chem_comp.id PYR
_chem_comp.name "PYRUVIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C3 H4 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 2023-11-03
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces PVL
_chem_comp.formula_weight 88.062
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PYR
_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 1AQ2
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
PYR C C1 C 0 1 N N N Y N Y 35.687 3.039 6.776 0.705 -0.157 0.002 C1 PYR 1
PYR O O1 O 0 1 N N N Y N Y 34.580 2.789 6.253 1.053 -1.318 0.001 O1 PYR 2
PYR OXT O2 O 0 1 N Y N Y N Y 36.677 3.339 6.077 1.628 0.822 -0.002 O2 PYR 3
PYR CA C2 C 0 1 N N N Y N N 35.836 2.980 8.201 -0.746 0.187 0.000 C2 PYR 4
PYR O3 O3 O 0 1 N Y N N N N 35.325 3.847 8.937 -1.092 1.344 0.001 O3 PYR 5
PYR CB C3 C 0 1 N N N N N N 36.646 1.906 8.739 -1.780 -0.910 -0.002 C3 PYR 6
PYR HXT HO2 H 0 1 N Y N Y N Y 36.430 3.336 5.160 2.556 0.551 -0.005 HO2 PYR 7
PYR HB1 H31 H 0 1 N N N N N N 36.710 2.007 9.833 -1.281 -1.879 -0.002 H31 PYR 8
PYR HB2 H32 H 0 1 N N N N N N 36.187 0.939 8.486 -2.404 -0.822 0.887 H32 PYR 9
PYR HB3 H33 H 0 1 N N N N N N 37.656 1.957 8.307 -2.402 -0.821 -0.892 H33 PYR 10
#
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
PYR C O DOUB N N 1
PYR C OXT SING N N 2
PYR C CA SING N N 3
PYR OXT HXT SING N N 4
PYR CA O3 DOUB N N 5
PYR CA CB SING N N 6
PYR CB HB1 SING N N 7
PYR CB HB2 SING N N 8
PYR CB HB3 SING N N 9
#
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
PYR SMILES ACDLabs 12.01 O=C(C(=O)O)C
PYR InChI InChI 1.03 InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)
PYR InChIKey InChI 1.03 LCTONWCANYUPML-UHFFFAOYSA-N
PYR SMILES_CANONICAL CACTVS 3.385 CC(=O)C(O)=O
PYR SMILES CACTVS 3.385 CC(=O)C(O)=O
PYR SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CC(=O)C(=O)O
PYR SMILES "OpenEye OEToolkits" 1.7.6 CC(=O)C(=O)O
#
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
PYR "SYSTEMATIC NAME" ACDLabs 12.01 "2-oxopropanoic acid"
PYR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "2-oxidanylidenepropanoic 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
PYR 'Create component' 1999-07-08 EBI
PYR 'Modify descriptor' 2011-06-04 RCSB
PYR 'Modify leaving atom flag' 2014-12-02 RCSB
PYR 'Modify leaving atom flag' 2017-11-15 RCSB
PYR 'Modify backbone' 2023-11-03 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id PYR
_pdbe_chem_comp_drugbank_details.drugbank_id DB00119
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Pyruvic acid'
_pdbe_chem_comp_drugbank_details.description
'An intermediate compound in the metabolism of carbohydrates, proteins, and fats. In thiamine deficiency, its oxidation is retarded and it accumulates in the tissues, especially in nervous structures. (From Stedman, 26th ed)'
_pdbe_chem_comp_drugbank_details.cas_number 127-17-3
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Pyruvate serves as a biological fuel by being converted to acetyl coenzyme A, which enters the tricarboxylic acid or Krebs cycle where it is metabolized to produce ATP aerobically. Energy can also be obtained anaerobically from pyruvate via its conversion to lactate. Pyruvate injections or perfusions increase contractile function of hearts when metabolizing glucose or fatty acids. This inotropic effect is striking in hearts stunned by ischemia/reperfusion. The inotropic effect of pyruvate requires intracoronary infusion. Among possible mechanisms for this effect are increased generation of ATP and an increase in ATP phosphorylation potential. Another is activation of pyruvate dehydrogenase, promoting its own oxidation by inhibiting pyruvate dehydrogenase kinase. Pyruvate dehydrogenase is inactivated in ischemia myocardium. Yet another is reduction of cytosolic inorganic phosphate concentration. Pyruvate, as an antioxidant, is known to scavenge such reactive oxygen species as hydrogen peroxide and lipid peroxides. Indirectly, supraphysiological levels of pyruvate may increase cellular reduced glutathione.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
PYR '2-ketopropionic acid' DrugBank ?
PYR '2-oxopropanoic acid' DrugBank ?
PYR 'a-Ketopropionic acid' DrugBank ?
PYR 'Acetylformic acid' DrugBank ?
PYR 'alpha-ketopropionic acid' DrugBank ?
PYR BTS DrugBank ?
PYR 'Pyroracemic acid' DrugBank ?
PYR 'α-ketopropionic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id PYR
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00119
_pdbe_chem_comp_drugbank_classification.parent 'Alpha-keto acids and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Keto acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as alpha-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the adjacent carbon.'
#
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
PYR DB00119 'Monocarboxylate transporter 4' Humans O15427 unknown 1
PYR DB00119 'Monocarboxylate transporter 8' Humans P36021 unknown 2
PYR DB00119 'Alanine--glyoxylate aminotransferase 2, mitochondrial' Humans Q9BYV1 unknown 3
PYR DB00119 'Monocarboxylate transporter 6' Humans O15375 unknown 4
PYR DB00119 'Pyruvate kinase PKLR' Humans P30613 unknown 5
PYR DB00119 'Monocarboxylate transporter 7' Humans O15403 unknown 6
PYR DB00119 'Monocarboxylate transporter 2' Humans O60669 unknown 7
PYR DB00119 'Pyruvate dehydrogenase E1 component subunit beta, mitochondrial' Humans P11177 unknown 8
PYR DB00119 'Pyruvate kinase PKM' Humans P14618 unknown 9
PYR DB00119 '4-aminobutyrate aminotransferase, mitochondrial' Humans P80404 unknown 10
PYR DB00119 'Monocarboxylate transporter 5' Humans O15374 unknown 11
PYR DB00119 'Monocarboxylate transporter 3' Humans O95907 unknown 12
PYR DB00119 'Monocarboxylate transporter 1' Humans P53985 unknown 13
PYR DB00119 'Pyruvate carboxylase, mitochondrial' Humans P11498 unknown 14
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
PYR C C 5.598 0.375 1
PYR O O 6.897 -0.375 2
PYR OXT O 5.598 1.875 3
PYR CA C 4.299 -0.375 4
PYR O3 O 4.299 -1.875 5
PYR CB C 3.000 0.375 6
#
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
PYR C O DOUBLE NONE 1
PYR C OXT SINGLE NONE 2
PYR C CA SINGLE NONE 3
PYR CA O3 DOUBLE NONE 4
PYR CA CB SINGLE NONE 5
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id PYR
_pdbe_chem_comp_rdkit_properties.exactmw 88.016
_pdbe_chem_comp_rdkit_properties.amw 88.062
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 6
_pdbe_chem_comp_rdkit_properties.NumAtoms 10
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 40.293
_pdbe_chem_comp_rdkit_properties.tpsa 54.370
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.340
_pdbe_chem_comp_rdkit_properties.CrippenMR 18.317
_pdbe_chem_comp_rdkit_properties.chi0v 2.725
_pdbe_chem_comp_rdkit_properties.chi1v 1.112
_pdbe_chem_comp_rdkit_properties.chi2v 0.185
_pdbe_chem_comp_rdkit_properties.chi3v 0.185
_pdbe_chem_comp_rdkit_properties.chi4v 0
_pdbe_chem_comp_rdkit_properties.chi0n 6.725
_pdbe_chem_comp_rdkit_properties.chi1n 3.021
_pdbe_chem_comp_rdkit_properties.chi2n 0.185
_pdbe_chem_comp_rdkit_properties.chi3n 0.185
_pdbe_chem_comp_rdkit_properties.chi4n 0
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.860
_pdbe_chem_comp_rdkit_properties.kappa1 1.330
_pdbe_chem_comp_rdkit_properties.kappa2 1.545
_pdbe_chem_comp_rdkit_properties.kappa3 1.458
_pdbe_chem_comp_rdkit_properties.Phi 0.342
#
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
PYR UniChem ChEMBL CHEMBL1162144
PYR UniChem DrugBank DB00119
PYR UniChem PDBe PYR
PYR UniChem 'Guide to Pharmacology' 4809
PYR UniChem 'KEGG LIGAND' C00022
PYR UniChem ChEBI 32816
PYR UniChem ZINC ZINC000001532517
PYR UniChem eMolecules 478132
PYR UniChem fdasrs 8558G7RUTR
PYR UniChem PharmGKB PA164778686
PYR UniChem HMDB HMDB0000243
PYR UniChem NMRShiftDB 20097599
PYR UniChem ACTor 127-17-3
PYR UniChem BindingDb 19473
PYR UniChem LipidMaps LMFA01060077
PYR UniChem MetaboLights MTBLC32816
PYR UniChem BRENDA 12318
PYR UniChem BRENDA 136939
PYR UniChem BRENDA 145520
PYR UniChem BRENDA 1725
PYR UniChem BRENDA 31
PYR UniChem ChemicalBook CB5257557
PYR UniChem ChemicalBook CB54635331
PYR UniChem rxnorm PYRUVATE
PYR UniChem rxnorm 'PYRUVIC ACID'
PYR UniChem MedChemExpress HY-Y0781
PYR UniChem 'Probes And Drugs' PD010233
PYR UniChem 'EPA CompTox Dashboard' DTXSID2021650
PYR UniChem SureChEMBL SCHEMBL1750
PYR UniChem 'PubChem TPHARMA' 15194194
PYR UniChem PubChem 1060
PYR UniChem Mcule MCULE-8587144313
PYR UniChem Nikkaji J2.015J
#
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
PYR C 1.058 -0.124 -0.109 ETKDGv3 1
PYR O 1.344 -0.617 1.015 ETKDGv3 2
PYR OXT 2.065 0.091 -1.045 ETKDGv3 3
PYR CA -0.331 0.226 -0.435 ETKDGv3 4
PYR O3 -0.599 0.718 -1.563 ETKDGv3 5
PYR CB -1.432 0.005 0.555 ETKDGv3 6
PYR HXT 3.028 -0.144 -0.837 ETKDGv3 7
PYR HB1 -2.408 0.328 0.132 ETKDGv3 8
PYR HB2 -1.494 -1.073 0.812 ETKDGv3 9
PYR HB3 -1.231 0.591 1.476 ETKDGv3 10
#