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Showing metabocard for 2-Amino-3,4-dihydroxypentanedioic acid (HMDB0030408)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:36:37 UTC
Update Date2022-03-07 02:52:32 UTC
HMDB IDHMDB0030408
Secondary Accession Numbers
  • HMDB30408
Metabolite Identification
Common Name2-Amino-3,4-dihydroxypentanedioic acid
Description2-Amino-3,4-dihydroxypentanedioic acid, also known as 3,4-dihydroxyglutamic acid or (3S,4S)-dhga, belongs to the class of organic compounds known as glutamic acid and derivatives. Glutamic acid and derivatives are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Based on a literature review a significant number of articles have been published on 2-Amino-3,4-dihydroxypentanedioic acid.
Structure
Data?1563861980
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0030408 (2-Amino-3,4-dihydroxypentanedioic acid)

  Mrv0541 05061305132D          

 12 11  0  0  0  0            999 V2000
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  2  0  0  0  0
 10  4  1  0  0  0  0
 11  5  2  0  0  0  0
 12  5  1  0  0  0  0
M  END
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3D MOL for HMDB0030408 (2-Amino-3,4-dihydroxypentanedioic acid)

HMDB0030408
     RDKit          3D
2-Amino-3,4-dihydroxypentanedioic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.2253   -0.4766   -1.3428 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2140   -0.6333   -0.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7806   -0.3357    1.0351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9771    0.0441    1.0994 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0740   -0.4519    2.2019 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0196    0.1666   -0.6210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1877    1.5146   -0.7369 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1487   -0.2157    0.3077 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3032   -1.5856    0.3980 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4349    0.4060   -0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3991   -0.3701   -0.3139 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5519    1.7875   -0.2852 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3774    0.5230   -1.5877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9182   -1.0563   -2.1387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9454   -1.7121   -0.3081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0513    0.2443    2.9328 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3667   -0.1798   -1.6423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4735    1.8044   -1.6416 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9508    0.1934    1.3246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0367   -1.9680    1.2651 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0128    2.3011    0.4689 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
 12 21  1  0
M  END
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3D SDF for HMDB0030408 (2-Amino-3,4-dihydroxypentanedioic acid)

  Mrv0541 05061305132D          

 12 11  0  0  0  0            999 V2000
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  7  2  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  2  0  0  0  0
 10  4  1  0  0  0  0
 11  5  2  0  0  0  0
 12  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0030408

> <DATABASE_NAME>
hmdb

> <SMILES>
NC(C(O)C(O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO6/c6-1(4(9)10)2(7)3(8)5(11)12/h1-3,7-8H,6H2,(H,9,10)(H,11,12)

> <INCHI_KEY>
SODSBJHVKSGOIZ-UHFFFAOYSA-N

> <FORMULA>
C5H9NO6

> <MOLECULAR_WEIGHT>
179.1281

> <EXACT_MASS>
179.042987025

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
14.888493838158086

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-3,4-dihydroxypentanedioic acid

> <ALOGPS_LOGP>
-3.30

> <JCHEM_LOGP>
-4.940481280579519

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.405647393356707

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.516363508425627

> <JCHEM_PKA_STRONGEST_BASIC>
8.625609582248906

> <JCHEM_POLAR_SURFACE_AREA>
141.08

> <JCHEM_REFRACTIVITY>
33.833400000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.03e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-3,4-dihydroxypentanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0030408 (2-Amino-3,4-dihydroxypentanedioic acid)

HMDB0030408
     RDKit          3D
2-Amino-3,4-dihydroxypentanedioic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.2253   -0.4766   -1.3428 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2140   -0.6333   -0.2984 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7806   -0.3357    1.0351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9771    0.0441    1.0994 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0740   -0.4519    2.2019 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0196    0.1666   -0.6210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1877    1.5146   -0.7369 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1487   -0.2157    0.3077 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3032   -1.5856    0.3980 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4349    0.4060   -0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3991   -0.3701   -0.3139 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5519    1.7875   -0.2852 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3774    0.5230   -1.5877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9182   -1.0563   -2.1387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9454   -1.7121   -0.3081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0513    0.2443    2.9328 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3667   -0.1798   -1.6423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4735    1.8044   -1.6416 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9508    0.1934    1.3246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0367   -1.9680    1.2651 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0128    2.3011    0.4689 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 10 12  1  0
  1 13  1  0
  1 14  1  0
  2 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
 12 21  1  0
M  END
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PDB for HMDB0030408 (2-Amino-3,4-dihydroxypentanedioic acid)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       4.001  -2.310   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
CONECT    1    2    4    6                                                  
CONECT    2    1    3    7                                                  
CONECT    3    2    5    8                                                  
CONECT    4    1    9   10                                                  
CONECT    5    3   11   12                                                  
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    5                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END
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3D PDB for HMDB0030408 (2-Amino-3,4-dihydroxypentanedioic acid)

COMPND    HMDB0030408
HETATM    1  N1  UNL     1      -2.225  -0.477  -1.343  1.00  0.00           N  
HETATM    2  C1  UNL     1      -1.214  -0.633  -0.298  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.781  -0.336   1.035  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.977   0.044   1.099  1.00  0.00           O  
HETATM    5  O2  UNL     1      -1.074  -0.452   2.202  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.020   0.167  -0.621  1.00  0.00           C  
HETATM    7  O3  UNL     1      -0.188   1.515  -0.737  1.00  0.00           O  
HETATM    8  C4  UNL     1       1.149  -0.216   0.308  1.00  0.00           C  
HETATM    9  O4  UNL     1       1.303  -1.586   0.398  1.00  0.00           O  
HETATM   10  C5  UNL     1       2.435   0.406  -0.117  1.00  0.00           C  
HETATM   11  O5  UNL     1       3.399  -0.370  -0.314  1.00  0.00           O  
HETATM   12  O6  UNL     1       2.552   1.787  -0.285  1.00  0.00           O  
HETATM   13  H1  UNL     1      -2.377   0.523  -1.588  1.00  0.00           H  
HETATM   14  H2  UNL     1      -1.918  -1.056  -2.139  1.00  0.00           H  
HETATM   15  H3  UNL     1      -0.945  -1.712  -0.308  1.00  0.00           H  
HETATM   16  H4  UNL     1      -1.051   0.244   2.933  1.00  0.00           H  
HETATM   17  H5  UNL     1       0.367  -0.180  -1.642  1.00  0.00           H  
HETATM   18  H6  UNL     1      -0.473   1.804  -1.642  1.00  0.00           H  
HETATM   19  H7  UNL     1       0.951   0.193   1.325  1.00  0.00           H  
HETATM   20  H8  UNL     1       1.037  -1.968   1.265  1.00  0.00           H  
HETATM   21  H9  UNL     1       3.013   2.301   0.469  1.00  0.00           H  
CONECT    1    2   13   14
CONECT    2    3    6   15
CONECT    3    4    4    5
CONECT    5   16
CONECT    6    7    8   17
CONECT    7   18
CONECT    8    9   10   19
CONECT    9   20
CONECT   10   11   11   12
CONECT   12   21
END
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SMILES for HMDB0030408 (2-Amino-3,4-dihydroxypentanedioic acid)

NC(C(O)C(O)C(O)=O)C(O)=O
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INCHI for HMDB0030408 (2-Amino-3,4-dihydroxypentanedioic acid)

InChI=1S/C5H9NO6/c6-1(4(9)10)2(7)3(8)5(11)12/h1-3,7-8H,6H2,(H,9,10)(H,11,12)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Amino-3,4-dihydroxypentanedioateGenerator
3,4-Dihydroxyglutamic acidHMDB
(3S,4S)-DHGAHMDB
3,4-Dihydroxy-L-glutamic acidHMDB
Chemical FormulaC5H9NO6
Average Molecular Weight179.1281
Monoisotopic Molecular Weight179.042987025
IUPAC Name2-amino-3,4-dihydroxypentanedioic acid
Traditional Name2-amino-3,4-dihydroxypentanedioic acid
CAS Registry NumberNot Available
SMILES
NC(C(O)C(O)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H9NO6/c6-1(4(9)10)2(7)3(8)5(11)12/h1-3,7-8H,6H2,(H,9,10)(H,11,12)
InChI KeySODSBJHVKSGOIZ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glutamic acid and derivatives. Glutamic acid and derivatives are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentGlutamic acid and derivatives
Alternative Parents
Substituents
  • Glutamic acid or derivatives
  • Alpha-amino acid
  • Amino fatty acid
  • Beta-hydroxy acid
  • Hydroxy fatty acid
  • Short-chain hydroxy acid
  • Alpha-hydroxy acid
  • Dicarboxylic acid or derivatives
  • Hydroxy acid
  • Monosaccharide
  • Fatty acid
  • Fatty acyl
  • 1,3-aminoalcohol
  • 1,2-diol
  • Amino acid
  • Secondary alcohol
  • Carboxylic acid
  • Hydrocarbon derivative
  • Alcohol
  • Organic oxide
  • Primary aliphatic amine
  • Carbonyl group
  • Organopnictogen compound
  • Organic oxygen compound
  • Amine
  • Primary amine
  • Organonitrogen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB002269
KNApSAcK IDNot Available
Chemspider ID11345033
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound22326306
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
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