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Showing NP-Card for (2s,4s)-2-amino-4,5-dihydroxypentanoic acid (NP0309060)

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Record Information
Version1.0
Created at2022-09-11 03:21:44 UTC
Updated at2022-09-11 03:21:44 UTC
NP-MRD IDNP0309060
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s,4s)-2-amino-4,5-dihydroxypentanoic acid
Description(2S,4S)-4,5-dihydroxynorvaline belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. (2s,4s)-2-amino-4,5-dihydroxypentanoic acid is found in Lunaria annua. Based on a literature review very few articles have been published on (2S,4S)-4,5-dihydroxynorvaline.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0309060 ((2s,4s)-2-amino-4,5-dihydroxypentanoic acid)


  Mrv1652309112205212D          

 10  9  0  0  1  0            999 V2000
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  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
    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
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    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
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  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 NP0309060 ((2s,4s)-2-amino-4,5-dihydroxypentanoic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.4321   -1.2130    1.0433 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3043   -0.0256    0.2233 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0033   -0.0974   -0.5413 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1225   -0.1713    0.4864 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1401    0.9320    1.3164 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4370   -0.2762   -0.2990 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6017    0.8837   -1.0780 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4634    0.1347   -0.6869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4182   -0.6820   -0.7118 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5285    1.2134   -1.5552 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0957   -2.0207    0.4667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8259   -1.0759    1.8776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2580    0.8671    0.8924 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0133   -1.0707   -1.0853 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1473    0.7550   -1.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0508   -1.1116    1.0707 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7106    0.7420    2.1874 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2369   -0.3726    0.4393 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3833   -1.1487   -0.9628 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0061    1.5993   -0.7343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5200    2.1384   -1.1367 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  7  1  0
  2  8  1  0
  8 10  1  0
  8  9  2  0
  1 11  1  0
  1 12  1  0
  2 13  1  1
  3 14  1  0
  3 15  1  0
  4 16  1  1
  5 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  0
 10 21  1  0
M  END
Download

3D SDF for NP0309060 ((2s,4s)-2-amino-4,5-dihydroxypentanoic acid)


  Mrv1652309112205212D          

 10  9  0  0  1  0            999 V2000
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  1  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
    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
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    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
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0309060

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO4/c6-4(5(9)10)1-3(8)2-7/h3-4,7-8H,1-2,6H2,(H,9,10)/t3-,4-/m0/s1

> <INCHI_KEY>
MNEGOIQRDZMOLW-IMJSIDKUSA-N

> <FORMULA>
C5H11NO4

> <MOLECULAR_WEIGHT>
149.146

> <EXACT_MASS>
149.068807838

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.151578477899278

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4S)-2-amino-4,5-dihydroxypentanoic acid

> <JCHEM_LOGP>
-4.457801293487577

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.242151404663868

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.084262551092107

> <JCHEM_PKA_STRONGEST_BASIC>
8.847897996117497

> <JCHEM_POLAR_SURFACE_AREA>
103.78000000000002

> <JCHEM_REFRACTIVITY>
32.8689

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4S)-2-amino-4,5-dihydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0309060 ((2s,4s)-2-amino-4,5-dihydroxypentanoic acid)

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PDB for NP0309060 ((2s,4s)-2-amino-4,5-dihydroxypentanoic acid)
HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  N   UNK     0       8.621   4.977   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.286   3.437   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    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6                                                            
CONECT    8    2    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 NP0309060 ((2s,4s)-2-amino-4,5-dihydroxypentanoic acid)
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SMILES for NP0309060 ((2s,4s)-2-amino-4,5-dihydroxypentanoic acid)
N[C@@H](C[C@H](O)CO)C(O)=O
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INCHI for NP0309060 ((2s,4s)-2-amino-4,5-dihydroxypentanoic acid)
InChI=1S/C5H11NO4/c6-4(5(9)10)1-3(8)2-7/h3-4,7-8H,1-2,6H2,(H,9,10)/t3-,4-/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC5H11NO4
Average Mass149.1460 Da
Monoisotopic Mass149.06881 Da
IUPAC Name(2S,4S)-2-amino-4,5-dihydroxypentanoic acid
Traditional Name(2S,4S)-2-amino-4,5-dihydroxypentanoic acid
CAS Registry NumberNot Available
SMILES
N[C@@H](C[C@H](O)CO)C(O)=O
InChI Identifier
InChI=1S/C5H11NO4/c6-4(5(9)10)1-3(8)2-7/h3-4,7-8H,1-2,6H2,(H,9,10)/t3-,4-/m0/s1
InChI KeyMNEGOIQRDZMOLW-IMJSIDKUSA-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
Lunaria annuaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentL-alpha-amino acids  
Alternative Parents
Substituents
  • L-alpha-amino acid
    • 

  • Short-chain hydroxy acid
    • 

  • Fatty acid
    • 

  • 1,3-aminoalcohol
    • 

  • 1,2-diol
    • 

  • Amino acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic nitrogen compound
    • 

  • Primary amine
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary aliphatic amine
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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-4.5ChemAxon
pKa (Strongest Acidic)2.08ChemAxon
pKa (Strongest Basic)8.85ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area103.78 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.87 m³·mol⁻¹ChemAxon
Polarizability14.15 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 ID9369491  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11194422  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]