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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:04:26 UTC
HMDB IDHMDB01370
Secondary Accession NumbersNone
Metabolite Identification
Common NameDiaminopimelic acid
DescriptionDiaminopimelic acid or DAPA is a lysine-like amino acid derivative that is a key component of the bacterial cell wall. DAPA is incorporated or integrated into peptidoglycan of gram negative bacteria and is the attachment point for Braun's lipoprotein (BLP or Murein Lipoprotein). BLP is found in gram-negative cell walls and is one of the most abundant membrane proteins. BLP is bound at its C-terminal end (a lysine) by a covalent bond to the peptidoglycan layer (specifically to diaminopimelic acid molecules) and is embedded in the outer membrane by its hydrophobic head (a cysteine with lipids attached). BLP tightly links the two layers and provides structural integrity to the bacterial outer membrane. Diaminopimelic acid can be found in human urine or feces due to the lysis or enzymatic breakdown of gram negative gut microbes.
Structure
Thumb
Synonyms
ValueSource
(S,S)-2,6-Diaminopimelic acidChEBI
(S-(R*,r*))-2,6-diaminoheptanedioic acidChEBI
L,L-2,6-Diaminopimelic acidChEBI
LL-2,6-DiaminopimelateChEBI
(S,S)-2,6-DiaminopimelateGenerator
LL-2,6-Diaminoheptanedioic acidGenerator
(S-(R*,r*))-2,6-diaminoheptanedioateGenerator
L,L-2,6-DiaminopimelateGenerator
LL-2,6-Diaminopimelic acidGenerator
( (R*,s*)-2,6-diamino-heptanedioateHMDB
( (R*,s*)-2,6-diamino-heptanedioic acidHMDB
(2R,6S)-2,6-diamino-HeptanedioateHMDB
(2R,6S)-2,6-diamino-Heptanedioic acidHMDB
(R*,s*)-2,6-diamino-heptanedioateHMDB
(R*,s*)-2,6-diamino-heptanedioic acidHMDB
2,6-diamino-HeptanedioateHMDB
2,6-diamino-Heptanedioic acidHMDB
2,6-DiaminoheptanedioateHMDB
2,6-Diaminoheptanedioic acidHMDB
2,6-DiaminopimelateHMDB
2,6-Diaminopimelic acidHMDB
a,A'-diaminopimelateHMDB
a,A'-diaminopimelic acidHMDB
a,e-DiaminopimelateHMDB
a,e-Diaminopimelic acidHMDB
D,L-DiaminopimelateHMDB
D,L-meso-DiaminoheptanedioateHMDB
D,L-meso-Diaminoheptanedioic acidHMDB
DAPAHMDB
DL-2,6-DiaminoheptanedioateHMDB
DL-2,6-Diaminoheptanedioic acidHMDB
DL-2,6-DiaminopimelateHMDB
DL-2,6-Diaminopimelic acidHMDB
L,L-2,6-DiaminoheptanedioateHMDB
L,L-2,6-Diaminoheptanedioic acidHMDB
L,L-DiaminopimelateHMDB
meso-1-alpha,epsilon-DiaminopimelateHMDB
meso-2,6-diamino-HeptanedioateHMDB
meso-2,6-diamino-Heptanedioic acidHMDB
meso-2,6-DiaminoheptanedioateHMDB
meso-2,6-Diaminoheptanedioic acidHMDB
meso-alpha,Alpha'-diaminopimelateHMDB
meso-alpha,Alpha'-diaminopimelic acidHMDB
meso-alpha,epsilon-DiaminopimelateHMDB
meso-alpha,epsilon-Diaminopimelic acidHMDB
meso-DiaminoheptanedioateHMDB
meso-Diaminoheptanedioic acidHMDB
meso-DiaminopimelateHMDB
Chemical FormulaC7H14N2O4
Average Molecular Weight190.1971
Monoisotopic Molecular Weight190.095356946
IUPAC Name(2S,6S)-2,6-diaminoheptanedioic acid
Traditional Namediamino-pimelic acid
CAS Registry Number583-93-7
SMILES
N[C@@H](CCC[C@H](N)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1
InChI KeyInChIKey=GMKMEZVLHJARHF-WHFBIAKZSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentL-alpha-amino acids
Alternative Parents
Substituents
  • L-alpha-amino acid
  • Medium-chain fatty acid
  • Amino fatty acid
  • Fatty acyl
  • Fatty acid
  • Dicarboxylic acid or derivatives
  • Carboxylic acid
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Microbial
Biofunction
  • Protein synthesis, amino acid biosynthesis
ApplicationNot Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility14.1 mg/mLALOGPS
logP-4.1ALOGPS
logP-5.5ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)1.85ChemAxon
pKa (Strongest Basic)9.83ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area126.64 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity43.64 m3·mol-1ChemAxon
Polarizability18.93 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0umi-1950000000-749403a0eb6d05c7903eView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0uk9-1980000000-1b092f9141e7549bee24View in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004l-0900000000-d85213bd7ac426f10cd7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-001i-9100000000-add590f1b216bdb40334View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-001i-9000000000-de98ed3bb8c48b6f9852View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot Available
Normal
  • Not Applicable
details
UrineDetected and Quantified0.08 +/-0.03 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022583
KNApSAcK IDNot Available
Chemspider ID388416
KEGG Compound IDC00666
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
NuGOwiki LinkHMDB01370
Metagene LinkHMDB01370
METLIN ID352
PubChem Compound439283
PDB IDNot Available
ChEBI ID16026
References
Synthesis ReferenceGao, Yong. Synthesis of diaminopimelic acid (DAP) and analogues: mechanistic studies on DAP aminotransferase, epimerase and dehydrogenase. (1998), 166 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Iida S, Taniguchi H, Kageyama A, Yazawa K, Chibana H, Murata S, Nomura F, Kroppenstedt RM, Mikami Y: Gordonia otitidis sp. nov., isolated from a patient with external otitis. Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):1871-6. [16166681 ]
  2. Ladesic B, Tomasic J, Kveder S, Hrsak I: The metabolic fate of 14C-labeled immunoadjuvant peptidoglycan monomer. II. In vitro studies. Biochim Biophys Acta. 1981 Nov 18;678(1):12-7. [6118181 ]
  3. Borruat G, Roten CA, Fay LB, Karamata D: A high-performance liquid chromatography method for the detection of diaminopimelic acid in urine. Anal Biochem. 2001 Apr 1;291(1):11-6. [11262151 ]
  4. Hamaker BR, Rivera K, Morales E, Graham GG: Effect of dietary fiber and starch on fecal composition in preschool children consuming maize, amaranth, or cassava flours. J Pediatr Gastroenterol Nutr. 1991 Jul;13(1):59-66. [1656007 ]