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Showing metabocard for D-Alanyl-D-alanine (HMDB0003459)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-12 21:25:35 UTC
Update Date2023-02-21 17:16:41 UTC
HMDB IDHMDB0003459
Secondary Accession Numbers
  • HMDB03459
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 ). D-Alanyl-D-alanine is a microbial metabolite.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003459 (D-Alanyl-D-alanine)

  Mrv0541 02231219442D          

 11 10  0  0  1  0            999 V2000
   18.6616  -20.6679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3761  -21.9055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.5195  -19.8429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.8051  -21.0805    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.9485  -20.6679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.0906  -20.6679    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.2341  -21.0805    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   20.0906  -19.8429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2341  -21.9055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3761  -21.0805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.5195  -20.6679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 10  2  0  0  0  0
  3 11  2  0  0  0  0
  6  4  1  1  0  0  0
  4 11  1  0  0  0  0
  7  5  1  6  0  0  0
  6  8  1  0  0  0  0
  6 10  1  0  0  0  0
  7  9  1  0  0  0  0
  7 11  1  0  0  0  0
M  END
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3D MOL for HMDB0003459 (D-Alanyl-D-alanine)

HMDB0003459
     RDKit          3D
D-Alanyl-D-alanine
 23 22  0  0  0  0  0  0  0  0999 V2000
   -2.9646    1.0402    0.3188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1207   -0.2162    0.4598 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2844   -1.0523   -0.7139 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7134    0.1702    0.6780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4372    0.8896    1.6550 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3230   -0.2567   -0.1937 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7052    0.0939   -0.0211 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2226    0.8557   -1.2192 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5436   -1.1353    0.1189 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9827   -2.2607    0.0728 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8996   -1.1007    0.2959 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4885    1.7833   -0.3391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0557    1.5014    1.3305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9695    0.7408   -0.0779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5020   -0.7360    1.3812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1603   -0.7441   -1.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4131   -2.0460   -0.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0710   -0.8545   -0.9999 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7783    0.7291    0.8836 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2889    1.1091   -0.9906 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6315    1.7596   -1.4269 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2582    0.1777   -2.1017 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4050   -0.4481    0.8697 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  1
  3 16  1  0
  3 17  1  0
  6 18  1  0
  7 19  1  1
  8 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
M  END
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3D SDF for HMDB0003459 (D-Alanyl-D-alanine)

  Mrv0541 02231219442D          

 11 10  0  0  1  0            999 V2000
   18.6616  -20.6679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3761  -21.9055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.5195  -19.8429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.8051  -21.0805    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.9485  -20.6679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.0906  -20.6679    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.2341  -21.0805    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   20.0906  -19.8429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2341  -21.9055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3761  -21.0805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.5195  -20.6679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2 10  2  0  0  0  0
  3 11  2  0  0  0  0
  6  4  1  1  0  0  0
  4 11  1  0  0  0  0
  7  5  1  6  0  0  0
  6  8  1  0  0  0  0
  6 10  1  0  0  0  0
  7  9  1  0  0  0  0
  7 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003459

> <DATABASE_NAME>
hmdb

> <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_KEY>
DEFJQIDDEAULHB-QWWZWVQMSA-N

> <FORMULA>
C6H12N2O3

> <MOLECULAR_WEIGHT>
160.1711

> <EXACT_MASS>
160.08479226

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
15.661226134276223

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-[(2R)-2-aminopropanamido]propanoic acid

> <ALOGPS_LOGP>
-2.64

> <JCHEM_LOGP>
-3.3796765186342177

> <ALOGPS_LOGS>
-0.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.8228437022597

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7263415407443627

> <JCHEM_PKA_STRONGEST_BASIC>
8.388610500766903

> <JCHEM_POLAR_SURFACE_AREA>
92.41999999999999

> <JCHEM_REFRACTIVITY>
37.794700000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.07e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-ala-D-ala

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0003459 (D-Alanyl-D-alanine)

HMDB0003459
     RDKit          3D
D-Alanyl-D-alanine
 23 22  0  0  0  0  0  0  0  0999 V2000
   -2.9646    1.0402    0.3188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1207   -0.2162    0.4598 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2844   -1.0523   -0.7139 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7134    0.1702    0.6780 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4372    0.8896    1.6550 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3230   -0.2567   -0.1937 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7052    0.0939   -0.0211 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2226    0.8557   -1.2192 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5436   -1.1353    0.1189 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9827   -2.2607    0.0728 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8996   -1.1007    0.2959 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4885    1.7833   -0.3391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0557    1.5014    1.3305 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9695    0.7408   -0.0779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5020   -0.7360    1.3812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1603   -0.7441   -1.2289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4131   -2.0460   -0.4259 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0710   -0.8545   -0.9999 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7783    0.7291    0.8836 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2889    1.1091   -0.9906 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6315    1.7596   -1.4269 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2582    0.1777   -2.1017 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4050   -0.4481    0.8697 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  1
  3 16  1  0
  3 17  1  0
  6 18  1  0
  7 19  1  1
  8 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
M  END
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PDB for HMDB0003459 (D-Alanyl-D-alanine)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      34.835 -38.580   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      36.169 -40.890   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      40.170 -37.040   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      38.836 -39.350   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      42.837 -38.580   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      37.502 -38.580   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      41.504 -39.350   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      37.502 -37.040   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      41.504 -40.890   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      36.169 -39.350   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      40.170 -38.580   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4    6   11                                                       
CONECT    5    7                                                            
CONECT    6    4    8   10                                                  
CONECT    7    5    9   11                                                  
CONECT    8    6                                                            
CONECT    9    7                                                            
CONECT   10    1    2    6                                                  
CONECT   11    3    4    7                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0003459 (D-Alanyl-D-alanine)

COMPND    HMDB0003459
HETATM    1  C1  UNL     1      -2.965   1.040   0.319  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.121  -0.216   0.460  1.00  0.00           C  
HETATM    3  N1  UNL     1      -2.284  -1.052  -0.714  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.713   0.170   0.678  1.00  0.00           C  
HETATM    5  O1  UNL     1      -0.437   0.890   1.655  1.00  0.00           O  
HETATM    6  N2  UNL     1       0.323  -0.257  -0.194  1.00  0.00           N  
HETATM    7  C4  UNL     1       1.705   0.094  -0.021  1.00  0.00           C  
HETATM    8  C5  UNL     1       2.223   0.856  -1.219  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.544  -1.135   0.119  1.00  0.00           C  
HETATM   10  O2  UNL     1       1.983  -2.261   0.073  1.00  0.00           O  
HETATM   11  O3  UNL     1       3.900  -1.101   0.296  1.00  0.00           O  
HETATM   12  H1  UNL     1      -2.489   1.783  -0.339  1.00  0.00           H  
HETATM   13  H2  UNL     1      -3.056   1.501   1.331  1.00  0.00           H  
HETATM   14  H3  UNL     1      -3.970   0.741  -0.078  1.00  0.00           H  
HETATM   15  H4  UNL     1      -2.502  -0.736   1.381  1.00  0.00           H  
HETATM   16  H5  UNL     1      -3.160  -0.744  -1.229  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.413  -2.046  -0.426  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.071  -0.855  -1.000  1.00  0.00           H  
HETATM   19  H8  UNL     1       1.778   0.729   0.884  1.00  0.00           H  
HETATM   20  H9  UNL     1       3.289   1.109  -0.991  1.00  0.00           H  
HETATM   21  H10 UNL     1       1.632   1.760  -1.427  1.00  0.00           H  
HETATM   22  H11 UNL     1       2.258   0.178  -2.102  1.00  0.00           H  
HETATM   23  H12 UNL     1       4.405  -0.448   0.870  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4   15
CONECT    3   16   17
CONECT    4    5    5    6
CONECT    6    7   18
CONECT    7    8    9   19
CONECT    8   20   21   22
CONECT    9   10   10   11
CONECT   11   23
END
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SMILES for HMDB0003459 (D-Alanyl-D-alanine)

C[C@@H](N)C(=O)N[C@H](C)C(O)=O
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INCHI for HMDB0003459 (D-Alanyl-D-alanine)

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
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
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 KeyDEFJQIDDEAULHB-QWWZWVQMSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentDipeptides
Alternative Parents
Substituents
  • Alpha-dipeptide
  • N-acyl-alpha-amino acid
  • N-acyl-alpha amino acid or derivatives
  • Alpha-amino acid amide
  • Alanine or derivatives
  • Alpha-amino acid or derivatives
  • Amino acid or derivatives
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Amino acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Primary aliphatic amine
  • Organic nitrogen compound
  • Carbonyl group
  • Primary amine
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available134.051http://allccs.zhulab.cn/database/detail?ID=AllCCS00000060
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Prostate Tissue
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
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. doi: 10.1038/nature07762. [PubMed:19212411 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB003740
KNApSAcK IDC00019576
Chemspider ID4573916
KEGG Compound IDC00993
BioCyc IDD-ALA-D-ALA
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6937
PubChem Compound5460362
PDB IDNot Available
ChEBI ID16576
Food Biomarker OntologyNot Available
VMH IDM03164
MarkerDB IDNot Available
Good Scents IDNot Available
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)Not Available
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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed:17267218 ]