You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version3.6
Creation Date2006-08-12 21:25:35 UTC
Update Date2016-02-11 01:06:18 UTC
HMDB IDHMDB03459
Secondary Accession NumbersNone
Metabolite Identification
Common NameD-Alanyl-D-alanine
DescriptionThe ATP-dependent carboxylate-amine/thiol ligase superfamily is known to contain enzymes catalyzing the formation of various types of peptide, one of which is d-alanyl-d-alanine.(PMID: 16030213 ). The glycopeptide antibiotic vancomycin acts by binding to the D-alanyl-D-alanine terminus of the cell wall precursor lipid II in the cytoplasmic membrane.(PMID: 17418637 ). D-alanine-D-alanine ligase from Thermotoga maritima ATCC 43589 (TmDdl) was a useful biocatalyst for synthesizing D-amino acid dipeptides.D-Alanine-D-alanine ligase (Ddl) catalyzes the biosynthesis of an essential bacterial peptidoglycan precursor D-alanyl-D-alanine and it represents an important target for development of new antibacterial drugs. (PMID: 17267218 ).
Structure
Thumb
Synonyms
ValueSource
(D-Ala)2ChEBI
D-Ala-D-alaChEBI
H-D-Ala-D-ala-OHChEBI
(2R)-2-[[(2R)-2-Aminopropanoyl]amino]propanoateGenerator
Alanyl-D-alanineHMDB
Chemical FormulaC6H12N2O3
Average Molecular Weight160.1711
Monoisotopic Molecular Weight160.08479226
IUPAC Name(2R)-2-[(2R)-2-aminopropanamido]propanoic acid
Traditional NameD-ala-D-ala
CAS Registry Number923-16-0
SMILES
C[C@@H](N)C(=O)N[C@H](C)C(O)=O
InChI Identifier
InChI=1S/C6H12N2O3/c1-3(7)5(9)8-4(2)6(10)11/h3-4H,7H2,1-2H3,(H,8,9)(H,10,11)/t3-,4-/m1/s1
InChI KeyInChIKey=DEFJQIDDEAULHB-QWWZWVQMSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as peptides. These are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentPeptides
Alternative Parents
Substituents
  • Alpha peptide
  • N-acyl-aliphatic-alpha amino acid
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboximidic acid derivative
  • Carboximidic 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
  • Endogenous
  • Microbial
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm (predicted from logP)
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility70.7 mg/mLALOGPS
logP-2.6ALOGPS
logP-3.4ChemAxon
logS-0.36ALOGPS
pKa (Strongest Acidic)3.73ChemAxon
pKa (Strongest Basic)8.39ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area92.42 Å2ChemAxon
Rotatable Bond Count3ChemAxon
Refractivity37.79 m3·mol-1ChemAxon
Polarizability15.66 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0296-5900000000-799966b5c9620715d16aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-9200000000-513a3e368e7c6334e54fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-006x-9000000000-0724d314ee5219f1c728View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-2900000000-b6d1f12edd1486d8cbb4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-059i-9600000000-8635adeca87ba2d6a666View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00du-9000000000-17647b2edc99cfa2d13bView in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Prostate Tissue
  • Saliva
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
SalivaDetected and Quantified0.119 +/- 0.176 uMAdult (>18 years old)Not Specified
Normal
    • Sugimoto et al. (...
details
SalivaDetected and Quantified0.184 +/- 0.138 uMAdult (>18 years old)Not Specified
Normal
    • Sugimoto et al. (...
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
Prostate TissueDetected and Quantified0.5 (0.0-1.0) umol/g tissueAdult (>18 years old)Both
Prostate cancer
details
Associated Disorders and Diseases
Disease References
Prostate cancer
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. [19212411 ]
Associated OMIM IDs
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB006399
KNApSAcK IDC00019576
Chemspider ID4573916
KEGG Compound IDC00993
BioCyc IDD-ALA-D-ALA
BiGG IDNot Available
Wikipedia LinkNot Available
NuGOwiki LinkHMDB03459
Metagene LinkHMDB03459
METLIN ID6937
PubChem Compound5460362
PDB IDNot Available
ChEBI ID16576
References
Synthesis ReferenceNeuhaus, Francis C. Enzymic synthesis of D-alanyl-D-alanine. Biochemical and Biophysical Research Communications (1960), 3 401-5.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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 ]
  2. Franken N, Seidl PH, Kuchenbauer T, Kolb HJ, Schleifer KH, Weiss L, Tympner KD: Specific immunoglobulin A antibodies to a peptide subunit sequence of bacterial cell wall peptidoglycan. Infect Immun. 1984 Apr;44(1):182-7. [6423541 ]
  3. Tabata K, Ikeda H, Hashimoto S: ywfE in Bacillus subtilis codes for a novel enzyme, L-amino acid ligase. J Bacteriol. 2005 Aug;187(15):5195-202. [16030213 ]
  4. Jansen A, Turck M, Szekat C, Nagel M, Clever I, Bierbaum G: Role of insertion elements and yycFG in the development of decreased susceptibility to vancomycin in Staphylococcus aureus. Int J Med Microbiol. 2007 Jul;297(4):205-15. Epub 2007 Apr 5. [17418637 ]
  5. Kovac A, Majce V, Lenarsic R, Bombek S, Bostock JM, Chopra I, Polanc S, Gobec S: Diazenedicarboxamides as inhibitors of D-alanine-D-alanine ligase (Ddl). Bioorg Med Chem Lett. 2007 Apr 1;17(7):2047-54. Epub 2007 Jan 17. [17267218 ]