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Showing NP-Card for D-Alanyl glycine (NP0046903)

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Record Information
Version1.0
Created at2022-03-17 20:31:26 UTC
Updated at2022-03-17 20:31:26 UTC
NP-MRD IDNP0046903
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Alanyl glycine
Description D-Alanyl glycine is found in Oryza punctata.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0046903 (D-Alanyl glycine)


  Mrv1533007131513452D          

 11 10  0  0  1  0            999 V2000
    2.0625    0.7145    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 C   0  0  2  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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   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
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  3  6  1  1  0  0  0
  7  2  1  4  0  0  0
  7  5  2  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
  3 11  1  1  0  0  0
M  END
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3D MOL for NP0046903 (D-Alanyl glycine)

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3D SDF for NP0046903 (D-Alanyl glycine)

  Mrv1533007131513452D          

 11 10  0  0  1  0            999 V2000
    2.0625    0.7145    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 C   0  0  2  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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   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
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  3  6  1  1  0  0  0
  7  2  1  4  0  0  0
  7  5  2  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  1  0  0  0  0
  3 11  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0046903

> <DATABASE_NAME>
NP-MRD

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

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

> <INCHI_KEY>
CXISPYVYMQWFLE-GSVOUGTGSA-N

> <FORMULA>
C5H10N2O3

> <MOLECULAR_WEIGHT>
146.146

> <EXACT_MASS>
146.06914219

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
14.077019377822126

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[(2R)-2-amino-1-hydroxypropylidene]amino}acetic acid

> <ALOGPS_LOGP>
-3.06

> <JCHEM_LOGP>
-3.348343236476017

> <ALOGPS_LOGS>
-1.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
4.308892928298567

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3699242212641978

> <JCHEM_PKA_STRONGEST_BASIC>
9.570041626934017

> <JCHEM_POLAR_SURFACE_AREA>
95.91

> <JCHEM_REFRACTIVITY>
33.8225

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.09e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{[(2R)-2-amino-1-hydroxypropylidene]amino}acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0046903 (D-Alanyl glycine)
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PDB for NP0046903 (D-Alanyl glycine)
HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.540   2.667   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      -3.080  -2.667   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -3.080   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       3.080   0.000   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    4    7                                                       
CONECT    3    1    5    6   11                                             
CONECT    4    2    8    9                                                  
CONECT    5    3    7   10                                                  
CONECT    6    3                                                            
CONECT    7    2    5                                                       
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    3                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END

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3D PDB for NP0046903 (D-Alanyl glycine)
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SMILES for NP0046903 (D-Alanyl glycine)
[H][C@](C)(N)C(O)=NCC(O)=O
Download
INCHI for NP0046903 (D-Alanyl glycine)
InChI=1S/C5H10N2O3/c1-3(6)5(10)7-2-4(8)9/h3H,2,6H2,1H3,(H,7,10)(H,8,9)/t3-/m1/s1
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View in JSmol
Synonyms
ValueSource
aGChEBI
Chemical FormulaC5H10N2O3
Average Mass146.1460 Da
Monoisotopic Mass146.06914 Da
IUPAC Name2-{[(2R)-2-amino-1-hydroxypropylidene]amino}acetic acid
Traditional Name{[(2R)-2-amino-1-hydroxypropylidene]amino}acetic acid
CAS Registry NumberNot Available
SMILES
[H][C@](C)(N)C(O)=NCC(O)=O
InChI Identifier
InChI=1S/C5H10N2O3/c1-3(6)5(10)7-2-4(8)9/h3H,2,6H2,1H3,(H,7,10)(H,8,9)/t3-/m1/s1
InChI KeyCXISPYVYMQWFLE-GSVOUGTGSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Oryza punctataLOTUS Database
Oryza sativaFooDB
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-3.1ALOGPS
logP-3.3ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)3.37ChemAxon
pKa (Strongest Basic)9.57ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area95.91 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity33.82 m³·mol⁻¹ChemAxon
Polarizability14.08 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 IDFDB006400  
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6992370  
PDB IDNot Available
ChEBI ID73836  
Good Scents IDNot Available
References
General ReferencesNot Available