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Human Metabolome Database Version 2.5

 

Showing metabocard for 5-Amino-2-oxopentanoic acid (HMDB06272)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2007-05-22 21:51:34
Update Date 2009-05-05 21:00:45
Accession Number HMDB06272
Secondary Accession Numbers Not Available
Common Name 5-Amino-2-oxopentanoic acid
Description 5-Amino-2-oxopentanoic acid is a breakdown product of D-proline. D-proline is first converted to 1-pyrroline-2-carboxylic acid via D-amino acid oxidase, which then spontaneously breaks down into 5-amino-2-oxopentanoic acid.
Synonyms
  1. 2-Oxo-5-amino-pentanoate
  2. 2-Oxo-5-aminopentanoate
  3. 2-Oxo-5-aminovalerate
  4. 5-Amino-2-oxopentanoic acid
  5. Alpha-keto-delta-aminopentanoate
  6. 5-Amino-2-oxopentanoate
  7. 2-Oxo-5-amino-pentanoic acid
  8. 2-Oxo-5-aminopentanoic acid
  9. Alpha-keto-delta-aminopentanoic acid
Chemical IUPAC Name 5-amino-2-oxo-pentanoate
Chemical Formula C5H9NO3
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Amino acids and Amino Acid conjugates
Class
  • Amino Acids
Sub Class
  • NA
Family
  • Mammalian Metabolite
Species
  • ketone
  • primary amine
  • primary aliphatic amine (alkylamine)
  • carboxylic acid
Biofunction
  • Protein synthesis, amino acid biosynthesis
Application
—
Source
  • Endogenous
Average Molecular Weight 131.130
Monoisotopic Molecular Weight 131.058243
Isomeric SMILES NCCCC(=O)C(O)=O
Canonical SMILES NCCCC(=O)C(O)=O
KEGG Compound ID C01110 Link Image
BioCyc ID 5-AMINO-2-OXOPENTANOATE Link Image
BiGG ID 36830 Link Image
Wikipedia Link Not Available
NuGOwiki Link HMDB06272 Link Image
Metagene Link HMDB06272 Link Image
METLIN ID Not Available
PubChem Compound 5459975 Link Image
PubChem Substance 4342 Link Image
ChEBI ID 17572 Link Image
CAS Registry Number Not Available
InChI Identifier InChI=1/C5H9NO3/c6-3-1-2-4(7)5(8)9/h1-3,6H2,(H,8,9)
Synthesis Reference Not Available
Melting Point (Experimental) Not Available
Experimental Water Solubility Not Available Source: PhysProp
Predicted Water Solubility 56.100002 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity Not Available Source: PhysProp
Predicted LogP/Hydrophobicity -2.46 [Predicted by ALOGPS] Calculated using ALOGPS
Material Safety Data Sheet (MSDS) Not Available
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Not Available
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Not Available
Predicted 1H NMR Spectrum Show Image
Show Peaklist
Predicted 13C NMR Spectrum Show Image
Show Peaklist
Mass Spectrum Not Available
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location
  • peroxisome
Biofluid Location Not Available
Tissue Location Not Available
Concentrations (Normal) Not Available
Concentrations (Abnormal) Not Available
Associated Disorders Not Available
OMIM ID Not Available
Pathways
Name SMPDB Link KEGG Link
D-Arginine and D-Ornithine Metabolism SMP00036 Link Image map00472 Link Image
Fatty Acid Elongation In Mitochondria SMP00054 Link Image map00062 Link Image
General References Not Available
Metabolic Enzymes
  1. 3-ketoacyl-CoA thiolase, mitochondrial
  2. D-amino-acid oxidase
  3. cDNA, FLJ93456, highly similar to Homo sapiens D-amino-acid oxidase (DAO), mRNA (D-amino-acid oxidase, isoform CRA_c)
Enzyme 1 [top]
Enzyme 1 ID 5260
Enzyme 1 Name 3-ketoacyl-CoA thiolase, mitochondrial
Enzyme 1 Synonyms
  1. Beta- ketothiolase
  2. Acetyl-CoA acyltransferase
  3. Mitochondrial 3-oxoacyl- CoA thiolase
  4. T1
Enzyme 1 Gene Name ACAA2
Enzyme 1 Protein Sequence >3-ketoacyl-CoA thiolase, mitochondrial 
MALLRGVFVVAAKRTPFGAYGGLLKDFTATDLSEFAAKAALSAGKVSPETVDSVIMGNVL
QSSSDAIYLARHVGLRVGIPKETPALTINRLCGSGFQSIVNGCQEICVKEAEVVLCGGTE
SMSQAPYCVRNVRFGTKLGSDIKLEDSLWVSLTDQHVQLPMAMTAENLAVKHKISREECD
KYALQSQQRWKAANDAGYFNDEMAPIEVKTKKGKQTMQVDEHARPQTTLEQLQKLPPVFK
KDGTVTAGNASGVADGAGAVIIASEDAVKKHNFTPLARIVGYFVSGCDPSIMGIGPVPAI
SGALKKAGLSLKDMDLVEVNEAFAPQYLAVERSLDLDISKTNVNGGAIALGHPLGGSGSR
ITAHLVHELRRRGGKYAVGSACIGGGQGIAVIIQSTA
Enzyme 1 Number of Residues 397
Enzyme 1 Molecular Weight 41925
Enzyme 1 Theoretical pI 8.21
Enzyme 1 GO Classification Not Available
Enzyme 1 General Function Lipid transport and metabolism
Enzyme 1 Specific Function Acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA
Enzyme 1 Pathways
  • Benzoate Degradation via Hydroxylation (map00362 Link Image)
  • Bile Acid Biosynthesis (map00120 Link Image)
  • Fatty Acid Elongation In Mitochondria (map00062 Link Image)
  • Fatty Acid Metabolism (map00071 Link Image)
  • Valine, Leucine and Isoleucine Degradation (map00280 Link Image)
Enzyme 1 Reactions
  • acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • 1-12
Enzyme 1 Transmembrane Regions Not Available
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 509676 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P42765 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name THIM_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1194 bp 
ATGCGTCTGCTCCGAGGTGTGTTTGTAGTTGCTGCTAAGCGAACGCCCTTTGGAGCTTAC
GGAGGCCTTCTGAAAGACTTCACTGCTACTGACTTGTCTGAATTTGCTGCCAAGGCTGCC
TTGTCTGCTGGCAAAGTCTCACCTGAAACAGTTGACAGTGTGATTATGGGCAATGTCCTG
CAGAGTTCTTCAGATGCTATATATTTGGCAAGGCATGTTGGTTTGCGTGTGGGAATCCCA
AAGGAGACCCCAGCTCTCACGATTAATAGGCTCTGTGGTTCTGGTTTTCAGTCCATTGTG
AATGGATGTCAGGAAATTTGTGTTAAAGAAGCTGAAGTTGTTTTATGTGGAGGAACCGAA
AGCATGAGCCAAGCTCCCTACTGTGTCAGAAATGTGCGTTTTGGAACCAAGCTTGGATCA
GATATCAAGCTGGAAGATTCTTTATGGGTATCATTAACAGATCAGCATGTCCAGCTCCCC
ATGGCAATGACTGCAGAGAATCTTACTGTAAAACACAAAATAAGCAGAGAAGAATGTGAC
AAATATGCCCTGCAGTCACAGCAGAGATGGAAAGCTGCTAATGATGCTGGCTACTTTAAT
GATGAAATGGCACCAATTGAAGTGAAGACAAAGAAAGGAAAACAGACAATGCAGGTAGAC
GAGCATGCTCGGCCCCAAACCACCCTGGAACAGTTACAGAAACTTCCTCCAGTATTCAAG
AAAGATGGAACTGTTACTGCAGGGAATGCATCGGGTGTAGCTGATGGTGCTGGAGCTGTT
ATCATAGCTAGTGAAGATGCTGTTAAGAAACATAACTTCACACCACTGGCAAGAATTGTG
GGCTACTTTGTATCTGGATGTGATCCCTCTATCATGGGTATTGGTCCTGTCCCTGCTATC
AGTGGGGCACTGAAGAAAGCAGGACTGAGTCTTAAGGACATGGATTTGGTAGAGGTGAAT
GAAGCTTTTGCTCCCCAGTACTTGGCTGTTGAGAGGAGTTTGGATCTTGACATAAGTAAA
ACCAATGTGAATGGAGGAGCCATTGCTTTGGGTCACCCACTGGGAGGATCTGGATCAAGA
ATTACTGCACACCTGGTTCACGAATTAAGGCGTCGAGGTGGAAAATATGCCGTTGGATCA
GCTTGCATTGGAGGTGGCCAAGGTATTGCTGTCATCATTCAGAGCACAGCCTGA
Enzyme 1 GenBank Gene ID D16294 Link Image
Enzyme 1 GeneCard ID ACAA2 Link Image
Enzyme 1 GenAtlas ID ACAA2 Link Image
Enzyme 1 HGNC ID HGNC:83 Link Image
Enzyme 1 Chromosome Location 18
Enzyme 1 Locus 18q21.1
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Abe H, Ohtake A, Yamamoto S, Satoh Y, Takayanagi M, Amaya Y, Takiguchi M, Sakuraba H, Suzuki Y, Mori M, et al.: Cloning and sequence analysis of a full length cDNA encoding human mitochondrial 3-oxoacyl-CoA thiolase. Biochim Biophys Acta. 1993 Nov 16;1216(2):304-6. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 5438
Enzyme 2 Name D-amino-acid oxidase
Enzyme 2 Synonyms
  1. DAMOX
  2. DAO
  3. DAAO
Enzyme 2 Gene Name DAO
Enzyme 2 Protein Sequence >D-amino-acid oxidase 
MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN
NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR
ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN
CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGG
IFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGP
SNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLSRMPPSHL
Enzyme 2 Number of Residues 347
Enzyme 2 Molecular Weight 39475
Enzyme 2 Theoretical pI 6.84
Enzyme 2 GO Classification
Function
  • D-amino-acid oxidase activity
  • catalytic activity
  • oxidoreductase activity
  • oxidoreductase activity, acting on the CH-NH2 group of donors
  • oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
Process
  • cellular metabolism
  • electron transport
  • generation of precursor metabolites and energy
  • metabolism
  • physiological process
Component
—
Enzyme 2 General Function Amino acid transport and metabolism
Enzyme 2 Specific Function Could act as a detoxifying agent which removes D-amino acids accumulated during aging. Acts on a variety of D-amino acids with a preference for those having small hydrophobic side chains followed by those bearing polar, aromatic, and basic groups. Does not act on acidic amino acids
Enzyme 2 Pathways
  • Arginine and Proline Metabolism (map00330 Link Image)
  • D-Arginine and D-ornithine Metabolism (map00472 Link Image)
  • Glycine, Serine and Threonine Metabolism (map00260 Link Image)
Enzyme 2 Reactions
  • a D-amino acid + H2O + O2 = a 2-oxo acid + ammonia + H2O2
Enzyme 2 Pfam Domain Function
Enzyme 2 Signals
  • 1-16
Enzyme 2 Transmembrane Regions Not Available
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 30446 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID P14920 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name OXDA_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence >1044 bp 
ATGCGTGTGGTGGTGATTGGAGCAGGAGTCATCGGGCTGTCCACCGCCCTCTGCATCCAT
GAGCGCTACCACTCAGTCCTGCAGCCACTGCACATAAAGGTCTACGCGGACCGCTTCACC
CCACTCACCACCACCGACGTGGCTGCCGGCCTCTGGCAGCCCTACCTTTCTGACCCCAAC
AACCCACAGGAGGCGGACTGGAGCCAACAGACCTTTGACTATCTCCTGAGCCATGTCCAT
TCTCCCAACGCTGAAAACCTGGGCCTGTTCCTAATCTCGGGCTACAACCTCTTCCATGAA
GCCATTCCGGACCCTTCCTGGAAGGACACAGTTCTGGGATTTCGGAAGCTGACCCCCAGA
GAGCTGGATATGTTCCCAGATTACGGCTATGGCTGGTTCCACACAAGCCTAATTCTGGAG
GGAAAGAACTATCTACAGTGGCTGACTGAAAGGTTAACTGAGAGGGGAGTGAAGTTCTTC
CAGCGGAAAGTGGAGTCTTTTGAGGAGGTGGCAAGAGAAGGCGCAGACGTGATTGTCAAC
TGCACTGGGGTATGGGCTGGGGCGCTACAACGAGACCCCCTGCTGCAGCCAGGCCGGGGG
CAGATCATGAAGGTGGACGCCCCTTGGATGAAGCACTTCATTCTCACCCATGACCCAGAG
AGAGGCATCTACAATTCCCCGTACATCATCCCAGGGACCCAGACAGTTACTCTTGGAGGC
ATCTTCCAGTTGGGAAACTGGAGTGAACTAAACAATATCCAGGACCACAACACCATTTGG
GAAGGCTGCTGCAGACTGGAGCCCACACTGAAGAATGCAAGAATTATTGGTGAAGCAACT
GGCTTCCGGCCAGTACGCCCCCAGATTCGGCTAGAAAGAGAACAGCTTCGCACTGGACCT
TCAAACACAGAGGTCATCCACAACTATGGCCATGGAGGCTACGGGCTCACCATCCACTGG
GGATGTGCCCTGGAGGCAGCCAAGCTCTTTGGGAGAATCCTGGAAGAAAAGAAATTGTCC
AGAATGCCACCATCCCACCTCTGA
Enzyme 2 GenBank Gene ID X13227 Link Image
Enzyme 2 GeneCard ID DAO Link Image
Enzyme 2 GenAtlas ID DAO Link Image
Enzyme 2 HGNC ID HGNC:2671 Link Image
Enzyme 2 Chromosome Location 12
Enzyme 2 Locus 12q24
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References
  1. Momoi K, Fukui K, Watanabe F, Miyake Y: Molecular cloning and sequence analysis of cDNA encoding human kidney D-amino acid oxidase. FEBS Lett. 1988 Sep 26;238(1):180-4. [PubMed Link Image]
  2. Fukui K, Miyake Y: Molecular cloning and chromosomal localization of a human gene encoding D-amino-acid oxidase. J Biol Chem. 1992 Sep 15;267(26):18631-8. [PubMed Link Image]
Enzyme 2 Metabolite References Not Available
Enzyme 3 [top]
Enzyme 3 ID 16461
Enzyme 3 Name cDNA, FLJ93456, highly similar to Homo sapiens D-amino-acid oxidase (DAO), mRNA (D-amino-acid oxidase, isoform CRA_c)
Enzyme 3 Synonyms Not Available
Enzyme 3 Gene Name DAO
Enzyme 3 Protein Sequence >cDNA, FLJ93456, highly similar to Homo sapiens D-amino-acid oxidase (DAO), mRNA (D-amino-acid oxidase, isoform CRA_c) 
MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN
NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR
ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN
CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGG
IFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGP
SNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLSRMPPSHL
Enzyme 3 Number of Residues 347
Enzyme 3 Molecular Weight 39475
Enzyme 3 Theoretical pI 6.84
Enzyme 3 GO Classification
Function
  • ATP binding
  • D-amino-acid oxidase activity
  • RNA ligase activity
  • adenyl nucleotide binding
  • binding
  • catalytic activity
  • ligase activity
  • ligase activity, forming phosphoric ester bonds
  • nucleotide binding
  • oxidoreductase activity
  • oxidoreductase activity, acting on the CH-NH2 group of donors
  • oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
  • purine nucleotide binding
  • tRNA ligase activity
Process
  • RNA metabolism
  • cellular metabolism
  • electron transport
  • generation of precursor metabolites and energy
  • metabolism
  • nucleobase, nucleoside, nucleotide and nucleic acid metabolism
  • physiological process
  • tRNA aminoacylation
  • tRNA aminoacylation for protein translation
  • tRNA metabolism
Component
—
Enzyme 3 General Function Amino acid transport and metabolism
Enzyme 3 Specific Function Not Available
Enzyme 3 Pathways Not Available
Enzyme 3 Reactions Not Available
Enzyme 3 Pfam Domain Function
Enzyme 3 Signals
  • None
Enzyme 3 Transmembrane Regions
  • None
Enzyme 3 Essentiality Not Available
Enzyme 3 GenBank ID Protein Not Available
Enzyme 3 UniProtKB/Swiss-Prot ID B2R7I5 Link Image
Enzyme 3 UniProtKB/Swiss-Prot Entry Name B2R7I5_HUMAN Link Image
Enzyme 3 PDB ID Not Available
Enzyme 3 Cellular Location Not Available
Enzyme 3 Gene Sequence Not Available
Enzyme 3 GenBank Gene ID AK312995 Link Image
Enzyme 3 GeneCard ID B2R7I5 Link Image
Enzyme 3 GenAtlas ID Not Available
Enzyme 3 HGNC ID Not Available
Enzyme 3 Chromosome Location 12
Enzyme 3 Locus 12q24
Enzyme 3 SNPs SNPJam Report Link Image
Enzyme 3 General References Not Available
Enzyme 3 Metabolite References Not Available