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Showing NP-Card for (2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid (NP0251351)

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Record Information
Version2.0
Created at2022-09-07 14:31:37 UTC
Updated at2022-09-07 14:31:37 UTC
NP-MRD IDNP0251351
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid
Description(2S,3Z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid 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,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid is found in Bankera fuligineoalba. Based on a literature review very few articles have been published on (2S,3Z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0251351 ((2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid)


  Mrv1652309072216312D          

 10  9  0  0  1  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    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
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  6  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 NP0251351 ((2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -1.5565    1.9984    0.1383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2711    1.2631    0.0149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1724   -0.0432    0.0273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4046   -0.8689    0.1725 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5617   -1.7122   -0.9540 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1147   -0.7527   -0.0938 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3311   -1.6435    1.0408 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2891    0.0974   -0.2538 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2408    0.0076    0.5608 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4618    1.0393   -1.2692 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3510    3.0677    0.3470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1804    1.6419    0.9816 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1566    1.9689   -0.8020 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6374    1.8364   -0.0897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3096   -0.2718    0.2956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3422   -1.5585    1.0412 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5197   -1.9868   -0.9517 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0532   -1.4093   -1.0011 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5599   -2.3047    1.1802 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6604   -1.1463    1.8736 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4774    0.7773   -2.2584 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  1  0
  6  8  1  0
  8 10  1  0
  8  9  2  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  6
  7 19  1  0
  7 20  1  0
 10 21  1  0
M  END
Download

3D SDF for NP0251351 ((2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid)


  Mrv1652309072216312D          

 10  9  0  0  1  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    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
   -0.4125    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  1  6  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>
NP0251351

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO3/c1-2-4(3-8)5(7)6(9)10/h2,5,8H,3,7H2,1H3,(H,9,10)/b4-2+/t5-/m0/s1

> <INCHI_KEY>
VCNVTZWONCZBGQ-FYTLMZHYSA-N

> <FORMULA>
C6H11NO3

> <MOLECULAR_WEIGHT>
145.158

> <EXACT_MASS>
145.073893218

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.440428202192294

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3Z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid

> <JCHEM_LOGP>
-3.114906404087801

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.127014727742374

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.3080127411428446

> <JCHEM_PKA_STRONGEST_BASIC>
8.626181441403036

> <JCHEM_POLAR_SURFACE_AREA>
83.55

> <JCHEM_REFRACTIVITY>
36.641600000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3Z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0251351 ((2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid)

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PDB for NP0251351 ((2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid)
HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770   1.334   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.310   1.334   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000  -2.667   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -3.080  -2.667   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -3.080   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    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 NP0251351 ((2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid)
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SMILES for NP0251351 ((2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid)
C\C=C(/CO)[C@H](N)C(O)=O
Download
INCHI for NP0251351 ((2s,3z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid)
InChI=1S/C6H11NO3/c1-2-4(3-8)5(7)6(9)10/h2,5,8H,3,7H2,1H3,(H,9,10)/b4-2+/t5-/m0/s1
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View in JSmol
Synonyms
ValueSource
(2S,3Z)-2-Amino-3-(hydroxymethyl)pent-3-enoateGenerator
Chemical FormulaC6H11NO3
Average Mass145.1580 Da
Monoisotopic Mass145.07389 Da
IUPAC Name(2S,3Z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid
Traditional Name(2S,3Z)-2-amino-3-(hydroxymethyl)pent-3-enoic acid
CAS Registry NumberNot Available
SMILES
C\C=C(/CO)[C@H](N)C(O)=O
InChI Identifier
InChI=1S/C6H11NO3/c1-2-4(3-8)5(7)6(9)10/h2,5,8H,3,7H2,1H3,(H,9,10)/b4-2+/t5-/m0/s1
InChI KeyVCNVTZWONCZBGQ-FYTLMZHYSA-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
Bankera fuligineoalbaLOTUS 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
    • 

  • Branched fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Short-chain hydroxy acid
    • 

  • Methyl-branched fatty acid
    • 

  • Unsaturated fatty acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • 1,3-aminoalcohol
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Primary amine
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Alcohol
    • 

  • Primary aliphatic amine
    • 

  • Organopnictogen compound
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • 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-3.1ChemAxon
pKa (Strongest Acidic)2.31ChemAxon
pKa (Strongest Basic)8.63ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area83.55 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity36.64 m³·mol⁻¹ChemAxon
Polarizability14.44 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound162874842  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]