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Showing NP-Card for (s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid (NP0261026)

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Record Information
Version1.0
Created at2022-09-08 03:22:05 UTC
Updated at2022-09-08 03:22:05 UTC
NP-MRD IDNP0261026
Secondary Accession NumbersNone
Natural Product Identification
Common Name(s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid
Description(2S)-2-[(1S,2S)-2-Hydroxy-3-cyclopentenyl]glycine 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. (s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid is found in Passiflora subpeltata. Based on a literature review very few articles have been published on (2S)-2-[(1S,2S)-2-Hydroxy-3-cyclopentenyl]glycine.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0261026 ((s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid)


  Mrv1652309082205222D          

 11 11  0  0  1  0            999 V2000
    1.2822    2.3518    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8612    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  6  2  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  6  0  0  0
M  END
Download

3D MOL for NP0261026 ((s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid)

     RDKit          3D

 22 22  0  0  0  0  0  0  0  0999 V2000
   -1.8997    1.2748   -0.7225 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2011    0.0423   -0.4217 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0505   -0.7657    0.4738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1669   -0.3266    0.8298 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6604   -2.0060    0.9441 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1044    0.4160    0.2263 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9701    1.2712   -0.6719 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3050    1.0729   -0.0459 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3318   -0.1090    0.5556 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0240   -0.8024    0.3864 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0117   -1.5216   -0.7969 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5790    2.0363   -0.0565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9273    1.1617   -0.5100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0623   -0.5034   -1.3741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2369   -2.8131    0.7124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0462    0.9213    1.1815 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9718    0.8968   -1.7164 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6544    2.3347   -0.6711 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1459    1.7507   -0.0530 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1669   -0.5240    1.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7297   -1.3946    1.2641 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4147   -2.4122   -0.6264 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
  2  3  1  0
  3  5  1  0
  3  4  2  0
 10  6  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  6
  6 16  1  1
  7 17  1  0
  7 18  1  0
  8 19  1  0
  9 20  1  0
 10 21  1  1
 11 22  1  0
  5 15  1  0
M  END
Download

3D SDF for NP0261026 ((s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid)


  Mrv1652309082205222D          

 11 11  0  0  1  0            999 V2000
    1.2822    2.3518    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1467    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8612    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  6  2  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0261026

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H]([C@@H]1CC=C[C@@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H11NO3/c8-6(7(10)11)4-2-1-3-5(4)9/h1,3-6,9H,2,8H2,(H,10,11)/t4-,5+,6+/m1/s1

> <INCHI_KEY>
PEAQTUDKZGSVCV-SRQIZXRXSA-N

> <FORMULA>
C7H11NO3

> <MOLECULAR_WEIGHT>
157.169

> <EXACT_MASS>
157.073893218

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
15.25621479647093

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-2-[(1S,2S)-2-hydroxycyclopent-3-en-1-yl]acetic acid

> <JCHEM_LOGP>
-3.0790600536743558

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.53609722512159

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.2472706316801325

> <JCHEM_PKA_STRONGEST_BASIC>
9.187649521881582

> <JCHEM_POLAR_SURFACE_AREA>
83.55000000000001

> <JCHEM_REFRACTIVITY>
39.426

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(S)-amino[(1S,2S)-2-hydroxycyclopent-3-en-1-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0261026 ((s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid)

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PDB for NP0261026 ((s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid)
HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  N   UNK     0       2.393   4.390   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.274   4.390   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.274   5.930   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -1.608   3.620   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6   11                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0261026 ((s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid)
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SMILES for NP0261026 ((s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid)
N[C@@H]([C@@H]1CC=C[C@@H]1O)C(O)=O
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INCHI for NP0261026 ((s)-amino[(1s,2s)-2-hydroxycyclopent-3-en-1-yl]acetic acid)
InChI=1S/C7H11NO3/c8-6(7(10)11)4-2-1-3-5(4)9/h1,3-6,9H,2,8H2,(H,10,11)/t4-,5+,6+/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC7H11NO3
Average Mass157.1690 Da
Monoisotopic Mass157.07389 Da
IUPAC Name(2S)-2-amino-2-[(1S,2S)-2-hydroxycyclopent-3-en-1-yl]acetic acid
Traditional Name(S)-amino[(1S,2S)-2-hydroxycyclopent-3-en-1-yl]acetic acid
CAS Registry NumberNot Available
SMILES
N[C@@H]([C@@H]1CC=C[C@@H]1O)C(O)=O
InChI Identifier
InChI=1S/C7H11NO3/c8-6(7(10)11)4-2-1-3-5(4)9/h1,3-6,9H,2,8H2,(H,10,11)/t4-,5+,6+/m1/s1
InChI KeyPEAQTUDKZGSVCV-SRQIZXRXSA-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
Passiflora subpeltataLOTUS 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
    • 

  • Secondary alcohol
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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)2.25ChemAxon
pKa (Strongest Basic)9.19ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area83.55 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity39.43 m³·mol⁻¹ChemAxon
Polarizability15.26 ųChemAxon
Number of Rings1ChemAxon
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 ID10276018  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound15922475  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]