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Showing NP-Card for (2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid (NP0232165)

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Record Information
Version2.0
Created at2022-09-06 13:18:20 UTC
Updated at2022-09-06 13:18:20 UTC
NP-MRD IDNP0232165
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid
DescriptionGly-D-Ala, also known as Ga, belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. (2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid is found in Blighia sapida. (2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid was first documented in 2017 (PMID: 28505407). Based on a literature review a small amount of articles have been published on Gly-D-Ala (PMID: 35530359) (PMID: 31879915).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0232165 ((2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid)


  Mrv1652309062215182D          

 10  9  0  0  1  0            999 V2000
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 N   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 O   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 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    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  2  0  0  0  0
  4  5  1  4  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 NP0232165 ((2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
   -1.9975   -0.8592    0.3763 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3068    0.4902    0.4944 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0751    0.3178    0.8196 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8717   -0.3510    0.0663 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3581   -0.9126   -1.0883 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2882   -0.4781    0.4815 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1657    0.0872   -0.5137 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4965    1.3002   -0.7371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4585    1.7146   -1.3136 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7312    1.6040   -1.2538 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3431   -1.6643    0.7570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9310   -0.8421    1.0032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2174   -1.0750   -0.6742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7729    1.0756    1.3230 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3540   -1.9070   -1.2481 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5243   -1.5744    0.5194 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4707   -0.0888    1.4813 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3213    1.1016   -0.4078 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0896   -0.3699   -0.5726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2638    2.4313   -1.0820 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  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
  1 13  1  0
  2 14  1  1
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
 10 20  1  0
M  END
Download

3D SDF for NP0232165 ((2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid)


  Mrv1652309062215182D          

 10  9  0  0  1  0            999 V2000
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 N   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 O   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 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    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  2  0  0  0  0
  4  5  1  4  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>
NP0232165

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10N2O3/c1-3(5(9)10)7-4(8)2-6/h3H,2,6H2,1H3,(H,7,8)(H,9,10)/t3-/m1/s1

> <INCHI_KEY>
VPZXBVLAVMBEQI-GSVOUGTGSA-N

> <FORMULA>
C5H10N2O3

> <MOLECULAR_WEIGHT>
146.146

> <EXACT_MASS>
146.06914219

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.890189877357807

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid

> <JCHEM_LOGP>
-3.3538834604746244

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
4.3104277724339894

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.446539935690561

> <JCHEM_PKA_STRONGEST_BASIC>
9.334336573300618

> <JCHEM_POLAR_SURFACE_AREA>
95.91000000000001

> <JCHEM_REFRACTIVITY>
33.8225

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0232165 ((2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid)

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PDB for NP0232165 ((2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic 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  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.540   0.000   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -0.770   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      -2.310  -1.334   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.620   2.667   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.620   0.000   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 NP0232165 ((2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid)
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SMILES for NP0232165 ((2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid)
C[C@@H](N=C(O)CN)C(O)=O
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INCHI for NP0232165 ((2r)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid)
InChI=1S/C5H10N2O3/c1-3(5(9)10)7-4(8)2-6/h3H,2,6H2,1H3,(H,7,8)(H,9,10)/t3-/m1/s1
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Synonyms
ValueSource
GaChEBI
Chemical FormulaC5H10N2O3
Average Mass146.1460 Da
Monoisotopic Mass146.06914 Da
IUPAC Name(2R)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid
Traditional Name(2R)-2-[(2-amino-1-hydroxyethylidene)amino]propanoic acid
CAS Registry NumberNot Available
SMILES
C[C@@H](N=C(O)CN)C(O)=O
InChI Identifier
InChI=1S/C5H10N2O3/c1-3(5(9)10)7-4(8)2-6/h3H,2,6H2,1H3,(H,7,8)(H,9,10)/t3-/m1/s1
InChI KeyVPZXBVLAVMBEQI-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
Blighia sapidaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentDipeptides  
Alternative Parents
Substituents
  • Alpha-dipeptide
    • 

  • N-acyl-alpha-amino acid
    • 

  • N-acyl-alpha amino acid or derivatives
    • 

  • Alpha-amino acid amide
    • 

  • Alanine or derivatives
    • 

  • Alpha-amino acid or derivatives
    • 

  • Amino acid or derivatives
    • 

  • Carboxamide group
    • 

  • Amino acid
    • 

  • Carboxylic acid salt
    • 

  • Secondary carboxylic acid amide
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic nitrogen compound
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Primary amine
    • 

  • Organic zwitterion
    • 

  • Primary aliphatic amine
    • 

  • Organic salt
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Organopnictogen compound
    • 

  • Amine
    • 

  • Organic oxygen compound
    • 

  • 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-3.4ChemAxon
pKa (Strongest Acidic)3.45ChemAxon
pKa (Strongest Basic)9.33ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area95.91 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity33.82 m³·mol⁻¹ChemAxon
Polarizability13.89 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 ID1267925  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound1551642  
PDB IDNot Available
ChEBI ID73891  
Good Scents IDNot Available
References
General References
  1. Chen Y, Su Y, Pang X, Song X, Zhao W, Yu M: Synthesis and Evaluation of Technetium-99m-Labeled pH (Low) Insertion Peptide Variant 7 for Early Diagnosis of MDA-MB-231 Triple-Negative Breast Cancer by Targeting the Tumor Microenvironment. Front Oncol. 2022 Apr 21;12:869260. doi: 10.3389/fonc.2022.869260. eCollection 2022. [PubMed:35530359  ] 
  2. Tymecka D, Misicka A: Solution Phase Peptide Synthesis: The Case of Biphalin. Methods Mol Biol. 2020;2103:1-11. doi: 10.1007/978-1-0716-0227-0_1. [PubMed:31879915  ] 
  3. Takeda K, Kemmoku K, Satoh Y, Ogasawara Y, Shin-Ya K, Dairi T: N-Phenylacetylation and Nonribosomal Peptide Synthetases with Substrate Promiscuity for Biosynthesis of Heptapeptide Variants, JBIR-78 and JBIR-95. ACS Chem Biol. 2017 Jul 21;12(7):1813-1819. doi: 10.1021/acschembio.7b00314. Epub 2017 May 19. [PubMed:28505407  ] 
  4. LOTUS database [Link]