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Showing NP-Card for l-pentahomoserine (NP0251227)

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Record Information
Version2.0
Created at2022-09-07 14:22:00 UTC
Updated at2022-09-07 14:22:00 UTC
NP-MRD IDNP0251227
Secondary Accession NumbersNone
Natural Product Identification
Common Namel-pentahomoserine
DescriptionL-Pentahomoserine, also known as 5-hydroxynorvaline or 5-OH-2-NH2-valerate, 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. L-Pentahomoserine is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0251227 (l-pentahomoserine)


  Mrv0541 02231216412D          

  9  8  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  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  0  0  0  0
  5  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
Download

3D MOL for NP0251227 (l-pentahomoserine)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
   -1.5719   -1.9088   -0.5086 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8144   -0.7667   -0.0101 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0965   -0.2851   -1.1053 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9151    0.8852   -0.6767 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7906    0.5812    0.5171 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6808   -0.4546    0.2358 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7298    0.2425    0.5214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9771    0.0559    0.4291 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3139    1.3992    1.1257 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5454   -1.6504   -0.7780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5622   -2.7048    0.1348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2034   -1.1591    0.8375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7726   -1.0924   -1.4633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5843    0.0485   -1.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6041    1.1500   -1.5235 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2958    1.7733   -0.4649 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1937    0.3066    1.3894 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4071    1.4655    0.7649 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2609   -0.1828   -0.5132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7149    2.2971    0.9519 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
  5  6  1  0
  2  7  1  0
  7  9  1  0
  7  8  2  0
  1 10  1  0
  1 11  1  0
  2 12  1  1
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  9 20  1  0
M  END
Download

3D SDF for NP0251227 (l-pentahomoserine)


  Mrv0541 02231216412D          

  9  8  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  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  0  0  0  0
  5  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0251227

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO3/c6-4(5(8)9)2-1-3-7/h4,7H,1-3,6H2,(H,8,9)/t4-/m0/s1

> <INCHI_KEY>
CZWARROQQFCFJB-BYPYZUCNSA-N

> <FORMULA>
C5H11NO3

> <MOLECULAR_WEIGHT>
133.1457

> <EXACT_MASS>
133.073893223

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
13.48352561153786

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-5-hydroxypentanoic acid

> <ALOGPS_LOGP>
-3.15

> <JCHEM_LOGP>
-3.3102086998554663

> <ALOGPS_LOGS>
0.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.972779968871116

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.355263439981361

> <JCHEM_PKA_STRONGEST_BASIC>
9.224033884543951

> <JCHEM_POLAR_SURFACE_AREA>
83.55000000000001

> <JCHEM_REFRACTIVITY>
31.551

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.68e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxy norvaline

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0251227 (l-pentahomoserine)

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PDB for NP0251227 (l-pentahomoserine)
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  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  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    2    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0251227 (l-pentahomoserine)
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SMILES for NP0251227 (l-pentahomoserine)
N[C@@H](CCCO)C(O)=O
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INCHI for NP0251227 (l-pentahomoserine)
InChI=1S/C5H11NO3/c6-4(5(8)9)2-1-3-7/h4,7H,1-3,6H2,(H,8,9)/t4-/m0/s1
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View in JSmol
Synonyms
ValueSource
2-Amino-5-hydroxypentanoic acidMeSH
5-HydroxynorvalineMeSH
alpha-Amino-delta-hydroxyvaleric acidMeSH
5-Hydroxy-2-aminovalerateMeSH
5-OH-2-NH2-ValerateMeSH
HAVA-5 CPDMeSH
2-Amino-5-hydroxyvaleric acid, (DL)-isomerMeSH
2-Amino-5-hydroxyvaleric acidMeSH
2-Amino-5-hydroxyvaleric acid, (L)-isomerMeSH
5-Hydroxy-2-aminovaleric acidMeSH
L-5-HydroxynorvalineChEMBL
(S)-2-Amino-5-hydroxypentanoateGenerator
(2S)-2-Amino-5-hydroxypentanoateGenerator
Chemical FormulaC5H11NO3
Average Mass133.1457 Da
Monoisotopic Mass133.07389 Da
IUPAC Name(2S)-2-amino-5-hydroxypentanoic acid
Traditional Name5-hydroxy norvaline
CAS Registry NumberNot Available
SMILES
N[C@@H](CCCO)C(O)=O
InChI Identifier
InChI=1S/C5H11NO3/c6-4(5(8)9)2-1-3-7/h4,7H,1-3,6H2,(H,8,9)/t4-/m0/s1
InChI KeyCZWARROQQFCFJB-BYPYZUCNSA-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 OriginNot Available
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
    • 

  • Fatty acid
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Primary amine
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Primary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • 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-3.2ALOGPS
logP-3.3ChemAxon
logS0.3ALOGPS
pKa (Strongest Acidic)2.36ChemAxon
pKa (Strongest Basic)9.22ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area83.55 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.55 m³·mol⁻¹ChemAxon
Polarizability13.48 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDDB03105  
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5287587  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]