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Showing NP-Card for (4r)-5-amino-4-hydroxy-2-oxopentanoic acid (NP0233921)

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Record Information
Version2.0
Created at2022-09-06 15:42:21 UTC
Updated at2022-09-06 15:42:21 UTC
NP-MRD IDNP0233921
Secondary Accession NumbersNone
Natural Product Identification
Common Name(4r)-5-amino-4-hydroxy-2-oxopentanoic acid
Description2-Oxo-4-hydroxy-5-aminovalerate belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms. 2-Oxo-4-hydroxy-5-aminovalerate is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. (4r)-5-amino-4-hydroxy-2-oxopentanoic acid is found in Daphnia pulex. Based on a literature review very few articles have been published on 2-Oxo-4-hydroxy-5-aminovalerate.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0233921 ((4r)-5-amino-4-hydroxy-2-oxopentanoic acid)


  Mrv1652309062217422D          

 10  9  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
Download

3D MOL for NP0233921 ((4r)-5-amino-4-hydroxy-2-oxopentanoic acid)

     RDKit          3D

 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.8559    0.8581    0.1716 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9223   -0.2298    0.1627 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4721    0.2693    0.0662 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4337    0.9805   -1.1460 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3681   -0.9587    0.0364 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8047   -0.7507   -0.0520 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5175   -1.8088   -0.0983 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4704    0.5347   -0.0901 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8641    1.6267   -0.0486 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8572    0.6091   -0.1774 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8106    0.4444    0.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7166    1.4583   -0.6660 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0088   -0.8349    1.0768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0704   -0.8875   -0.7040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2935    0.9418    0.9037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9324    0.4509   -1.7991 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0024   -1.6008   -0.8006 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1595   -1.5202    0.9862 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4725    0.4174    0.6000 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
  3  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8 10  1  0
  8  9  2  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  1
  4 16  1  0
  5 17  1  0
  5 18  1  0
 10 19  1  0
M  END
Download

3D SDF for NP0233921 ((4r)-5-amino-4-hydroxy-2-oxopentanoic acid)


  Mrv1652309062217422D          

 10  9  0  0  1  0            999 V2000
    1.7605    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0233921

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO4/c6-2-3(7)1-4(8)5(9)10/h3,7H,1-2,6H2,(H,9,10)/t3-/m1/s1

> <INCHI_KEY>
ICMJZHFYQVZYQN-GSVOUGTGSA-N

> <FORMULA>
C5H9NO4

> <MOLECULAR_WEIGHT>
147.13

> <EXACT_MASS>
147.053157774

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
13.320223457877407

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R)-5-amino-4-hydroxy-2-oxopentanoic acid

> <JCHEM_LOGP>
-3.51466010439521

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.726756657705003

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.8638061670010067

> <JCHEM_PKA_STRONGEST_BASIC>
9.178299338089634

> <JCHEM_POLAR_SURFACE_AREA>
100.62

> <JCHEM_REFRACTIVITY>
32.011300000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R)-5-amino-4-hydroxy-2-oxopentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0233921 ((4r)-5-amino-4-hydroxy-2-oxopentanoic acid)

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PDB for NP0233921 ((4r)-5-amino-4-hydroxy-2-oxopentanoic acid)
HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  N   UNK     0       3.286   3.437   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0233921 ((4r)-5-amino-4-hydroxy-2-oxopentanoic acid)
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SMILES for NP0233921 ((4r)-5-amino-4-hydroxy-2-oxopentanoic acid)
NC[C@H](O)CC(=O)C(O)=O
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INCHI for NP0233921 ((4r)-5-amino-4-hydroxy-2-oxopentanoic acid)
InChI=1S/C5H9NO4/c6-2-3(7)1-4(8)5(9)10/h3,7H,1-2,6H2,(H,9,10)/t3-/m1/s1
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View in JSmol
Synonyms
ValueSource
2-oxo-4-Hydroxy-5-aminovaleric acidGenerator
Chemical FormulaC5H9NO4
Average Mass147.1300 Da
Monoisotopic Mass147.05316 Da
IUPAC Name(4R)-5-amino-4-hydroxy-2-oxopentanoic acid
Traditional Name(4R)-5-amino-4-hydroxy-2-oxopentanoic acid
CAS Registry NumberNot Available
SMILES
NC[C@H](O)CC(=O)C(O)=O
InChI Identifier
InChI=1S/C5H9NO4/c6-2-3(7)1-4(8)5(9)10/h3,7H,1-2,6H2,(H,9,10)/t3-/m1/s1
InChI KeyICMJZHFYQVZYQN-GSVOUGTGSA-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
Daphnia pulexLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassKeto acids and derivatives  
Sub ClassShort-chain keto acids and derivatives  
Direct ParentShort-chain keto acids and derivatives  
Alternative Parents
Substituents
  • Short-chain keto acid
    • 

  • Alpha-keto acid
    • 

  • Beta-hydroxy ketone
    • 

  • Gamma-aminoketone
    • 

  • Alpha-hydroxy ketone
    • 

  • 1,2-aminoalcohol
    • 

  • Amino acid or derivatives
    • 

  • Ketone
    • 

  • Secondary alcohol
    • 

  • Amino acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Organopnictogen compound
    • 

  • Alcohol
    • 

  • Amine
    • 

  • Organooxygen compound
    • 

  • Primary amine
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • 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-3.5ChemAxon
pKa (Strongest Acidic)2.86ChemAxon
pKa (Strongest Basic)9.18ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area100.62 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.01 m³·mol⁻¹ChemAxon
Polarizability13.32 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID389694  
KEGG Compound IDC05941  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440852  
PDB IDNot Available
ChEBI ID1241  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]