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Showing NP-Card for (2s,4r)-2-amino-4-hydroxypentanedioic acid (NP0219043)

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Record Information
Version2.0
Created at2022-09-05 19:54:41 UTC
Updated at2022-09-05 19:54:41 UTC
NP-MRD IDNP0219043
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s,4r)-2-amino-4-hydroxypentanedioic acid
Description4-Hydroxy-L-glutamic acid, also known as 4-hydroxy-L-glutamate or L-erythro-4-hydroxyglutamate, 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. Specifically, 4-hydroxy-L-glutamic acid combines with 2-oxoglutarate to produce 4-hydroxy-2-oxoglutarate and glutamate. 4-Hydroxy-L-glutamic acid is a very strong basic compound (based on its pKa). Within humans, 4-hydroxy-L-glutamic acid participates in a number of enzymatic reactions. In particular, 4-hydroxy-L-glutamic acid can be biosynthesized from pyrroline hydroxycarboxylic acid through its interaction with the enzyme Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial. In addition, 4-hydroxy-L-glutamic acid can be converted into L-4-hydroxyglutamate semialdehyde through its interaction with the enzyme proline dehydrogenase 1, mitochondrial. In humans, 4-hydroxy-L-glutamic acid is involved in the metabolic disorder called the arginine: Glycine amidinotransferase deficiency (agat deficiency) pathway. 4-Hydroxy-L-glutamic acid is an intermediate in the metabolism of gamma-hydroxyglutamic acid. This reaction is catalyzed by 4-Hydroxy-L-glutamic acid aminotransferase (PMID: 13948827 ). (2s,4r)-2-amino-4-hydroxypentanedioic acid is found in Linaria vulgaris. (2s,4r)-2-amino-4-hydroxypentanedioic acid was first documented in 1962 (PMID: 13948827). The reaction can be described as: 4-Hydroxy-L-glutamate + 2-oxoglutarate <=> 4-hydroxy-2-oxoglutarate + L-glutamate.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0219043 ((2s,4r)-2-amino-4-hydroxypentanedioic acid)


  Mrv1652303062020152D          

 11 10  0  0  0  0            999 V2000
 9999.2842 9999.7990    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.998910000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7136 9999.7990    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10001.431410000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.1451 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.431410001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.7136 9998.9737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.569510000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8548 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.569510001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2842 9998.9737    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  1 11  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  7  1  6  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  END
Download

3D MOL for NP0219043 ((2s,4r)-2-amino-4-hydroxypentanedioic acid)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
    1.2170    1.6410    0.3468 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2662    0.1962    0.2420 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0525   -0.3101   -0.3080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2090    0.0684    0.5898 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2665    1.4360    0.6860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4429   -0.4362   -0.0495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3248    0.3742   -0.4005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6254   -1.8060   -0.2613 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3530   -0.1593   -0.6944 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0461    0.7245   -1.2430 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6112   -1.4814   -0.9712 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9286    1.9911    1.2637 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6881    2.0727   -0.4251 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4650   -0.2276    1.2551 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2228    0.1796   -1.2820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0142   -1.3942   -0.4952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0710   -0.4288    1.5726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4398    1.6885    1.6322 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3046   -2.1643   -0.9132 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3982   -1.9642   -0.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  1  0
  6  8  1  0
  6  7  2  0
  2  9  1  0
  9 11  1  0
  9 10  2  0
  1 12  1  0
  1 13  1  0
  2 14  1  1
  3 15  1  0
  3 16  1  0
  4 17  1  1
  5 18  1  0
  8 19  1  0
 11 20  1  0
M  END
Download

3D SDF for NP0219043 ((2s,4r)-2-amino-4-hydroxypentanedioic acid)


  Mrv1652303062020152D          

 11 10  0  0  0  0            999 V2000
 9999.2842 9999.7990    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.998910000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7136 9999.7990    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10001.431410000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.1451 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.431410001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.7136 9998.9737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.569510000.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8548 9999.7990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.569510001.0362    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2842 9998.9737    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  1 11  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  7  1  6  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0219043

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H](C[C@@H](O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO5/c6-2(4(8)9)1-3(7)5(10)11/h2-3,7H,1,6H2,(H,8,9)(H,10,11)/t2-,3+/m0/s1

> <INCHI_KEY>
HBDWQSHEVMSFGY-STHAYSLISA-N

> <FORMULA>
C5H9NO5

> <MOLECULAR_WEIGHT>
163.1287

> <EXACT_MASS>
163.048072403

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.014612264842874

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R)-2-amino-4-hydroxypentanedioic acid

> <ALOGPS_LOGP>
-3.67

> <JCHEM_LOGP>
-4.246000214409296

> <ALOGPS_LOGS>
-0.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.611738188377349

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6839758422188136

> <JCHEM_PKA_STRONGEST_BASIC>
9.160931011999752

> <JCHEM_POLAR_SURFACE_AREA>
120.85000000000001

> <JCHEM_REFRACTIVITY>
32.7363

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.43e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4R)-2-amino-4-hydroxypentanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0219043 ((2s,4r)-2-amino-4-hydroxypentanedioic acid)

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PDB for NP0219043 ((2s,4r)-2-amino-4-hydroxypentanedioic acid)
HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  C   UNK     0    8665.3318666.291   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8666.6658667.061   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8667.9998666.291   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8669.3398667.061   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8670.6718666.291   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8669.3398668.601   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8667.9998664.751   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8663.9968667.061   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0    8662.6628666.291   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8663.9968668.601   0.000  0.00  0.00           O+0
HETATM   11  N   UNK     0    8665.3318664.751   0.000  0.00  0.00           N+0
CONECT    1    2    8   11                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3                                                            
CONECT    8    1    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    1                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0219043 ((2s,4r)-2-amino-4-hydroxypentanedioic acid)
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SMILES for NP0219043 ((2s,4r)-2-amino-4-hydroxypentanedioic acid)
N[C@@H](C[C@@H](O)C(O)=O)C(O)=O
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INCHI for NP0219043 ((2s,4r)-2-amino-4-hydroxypentanedioic acid)
InChI=1S/C5H9NO5/c6-2(4(8)9)1-3(7)5(10)11/h2-3,7H,1,6H2,(H,8,9)(H,10,11)/t2-,3+/m0/s1
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View in JSmol
Synonyms
ValueSource
(2S,4R)-2-Amino-4-hydroxypentanedioic acidChEBI
L-Erythro-4-hydroxyglutamic acidChEBI
(2S,4R)-2-Amino-4-hydroxypentanedioateGenerator
L-Erythro-4-hydroxyglutamateGenerator
4-Hydroxy-L-glutamateGenerator
Erythro-4-hydroxy-L-glutamateHMDB
(4R)-4-Hydroxy-L-glutamateHMDB
(4R)-4-Hydroxy-L-glutamic acidHMDB
2-Hydroxy-4-aminoglutarateHMDB
2-Hydroxy-4-aminoglutaric acidHMDB
4-HydroxyglutamateHMDB
4-Hydroxyglutamic acidHMDB
Erythro-4-hydroxy-L-glutamic acidHMDB
(2S)-2-Amino-4-hydroxypentanedioic acidHMDB
gamma-Hydroxyglutamic acidHMDB
Γ-hydroxyglutamic acidHMDB
4-Hydroxy-L-glutamic acidHMDB
Chemical FormulaC5H9NO5
Average Mass163.1287 Da
Monoisotopic Mass163.04807 Da
IUPAC Name(2S,4R)-2-amino-4-hydroxypentanedioic acid
Traditional Name(2S,4R)-2-amino-4-hydroxypentanedioic acid
CAS Registry NumberNot Available
SMILES
N[C@@H](C[C@@H](O)C(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H9NO5/c6-2(4(8)9)1-3(7)5(10)11/h2-3,7H,1,6H2,(H,8,9)(H,10,11)/t2-,3+/m0/s1
InChI KeyHBDWQSHEVMSFGY-STHAYSLISA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Linaria vulgarisLOTUS Database
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
    • 

  • L-alpha-amino acid
    • 

  • Amino fatty acid
    • 

  • Short-chain hydroxy acid
    • 

  • Hydroxy fatty acid
    • 

  • Alpha-hydroxy acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Hydroxy acid
    • 

  • 1,3-aminoalcohol
    • 

  • Amino acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Organic nitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Primary amine
    • 

  • Hydrocarbon derivative
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Amine
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-3.7ALOGPS
logP-4.2ChemAxon
logS-0.34ALOGPS
pKa (Strongest Acidic)1.68ChemAxon
pKa (Strongest Basic)9.16ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area120.85 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.74 m³·mol⁻¹ChemAxon
Polarizability14.01 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0002273  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022938  
KNApSAcK IDNot Available
Chemspider ID389696  
KEGG Compound IDC03079  
BioCyc IDL-ERYTHRO-4-HYDROXY-GLUTAMATE  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440854  
PDB IDNot Available
ChEBI ID21285  
Good Scents IDNot Available
References
General References
  1. GOLDSTONE A, ADAMS E: Metabolism of gamma-hydroxyglutamic acid. I. Conversion to alpha-hydroxy-gamma-ketoglutarate by purified glutamic-aspartic transaminase to rat liver. J Biol Chem. 1962 Nov;237:3476-85. [PubMed:13948827  ] 
  2. LOTUS database [Link]