Showing metabocard for D-Alanyl-D-alanine (MMDBc0029715)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:38:44 UTC
Update Date2024-04-30 19:41:02 UTC
Metabolite IDMMDBc0029715
Metabolite Identification
Common NameD-Alanyl-D-alanine
DescriptionD-Alanyl-D-alanine is a component of peptidoglycan. The 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 )
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fdb1a22c6b0>


  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 #<Metabolite:0x00007fdb1a22c6b0>

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 #<Metabolite:0x00007fdb1a22c6b0>


  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>
MMDBc0029715

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007fdb1a22c6b0>

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 #<Metabolite:0x00007fdb1a22c6b0>

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 #<Metabolite:0x00007fdb1a22c6b0>

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 #<Metabolite:0x00007fdb1a22c6b0>

C[C@@H](N)C(=O)N[C@H](C)C(O)=O
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INCHI for #<Metabolite:0x00007fdb1a22c6b0>

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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Synonyms
ValueSource
(D-Ala)2ChEBI
D-Ala-D-alaChEBI
H-D-Ala-D-ala-OHChEBI
Alanyl-D-alanineHMDB
Ala-alaHMDB
H-Ala-ala-OHHMDB
AlanylalanineHMDB
Alanylalanine, (D)-isomerHMDB
Alanylalanine, (D-ala)-(L-ala)-isomerHMDB
Alanylalanine, (L)-isomerHMDB
Alanylalanine, (L-ala)-(D-ala)-isomerHMDB
Alanylalanine, (L-ala)-(DL-ala)-isomerHMDB
DialanineHMDB
D-Alanyl-L-alanineHMDB
L-Alanyl-D-alanineHMDB
Di-L-alanineHMDB
D-AlanylalanineHMDB
L-Alanyl-L-alanineHMDB
N-D-Alanyl-L-alanineHMDB
N-L-Alanyl-D-alanineHMDB
Molecular FormulaC6H12N2O3
Average Mass160.1711
Monoisotopic Mass160.08479226
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