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Showing NP-Card for S-ureidoglycine (NP0334383)

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Record Information
Version2.0
Created at2024-09-09 23:25:53 UTC
Updated at2024-09-09 23:25:53 UTC
NP-MRD IDNP0334383
Secondary Accession NumbersNone
Natural Product Identification
Common NameS-ureidoglycine
DescriptionS-ureidoglycine is a member of the class of compounds known as N-carbamoyl-alpha amino acids. N-carbamoyl-alpha amino acids are compounds containing an alpha amino acid which bears an carbamoyl group at its terminal nitrogen atom. S-ureidoglycine can be found in a number of food items such as green vegetables, spinach, millet, and japanese pumpkin, which makes S-ureidoglycine a potential biomarker for the consumption of these food products.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0334383 (S-ureidoglycine)


  Mrv2104 05252301582D          

  9  8  0  0  0  0            999 V2000
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.3020    0.0000 C   0  3  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -1.5395    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  6  1  0  0  0  0
  2  7  2  0  0  0  0
  2  8  1  0  0  0  0
  3  5  2  0  0  0  0
  3  6  1  0  0  0  0
  3  9  1  0  0  0  0
M  CHG  2   2   1   9  -1
M  RAD  1   4   3
M  END
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3D MOL for NP0334383 (S-ureidoglycine)

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3D SDF for NP0334383 (S-ureidoglycine)

  Mrv2104 05252301582D          

  9  8  0  0  0  0            999 V2000
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270   -0.3020    0.0000 C   0  3  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -1.5395    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1270    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  4  1  0  0  0  0
  1  6  1  0  0  0  0
  2  7  2  0  0  0  0
  2  8  1  0  0  0  0
  3  5  2  0  0  0  0
  3  6  1  0  0  0  0
  3  9  1  0  0  0  0
M  CHG  2   2   1   9  -1
M  RAD  1   4   3
M  END
> <DATABASE_ID>
NP0334383

> <DATABASE_NAME>
NP-MRD

> <INCHI_IDENTIFIER>
InChI=1/C3H5N3O3/c4-1(2(7)8)6-3(5)9/h1H,(H,7,8)(H3,5,6,9)/q+1/p-1

> <INCHI_KEY>
AJONJFGFTGGKEX-UHFFFAOYNA-M

> <FORMULA>
C3H4N3O3

> <MOLECULAR_WEIGHT>
130.083

> <EXACT_MASS>
130.025266001

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
10.293113710249807

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[1-(carboximidatoamino)-2-hydroxy-2-oxoethan-2-ium-1-yl]azanylidene

> <JCHEM_LOGP>
-3.8961158921404606

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.744168914116607

> <JCHEM_PKA_STRONGEST_ACIDIC>
-1.2304328593963814

> <JCHEM_PKA_STRONGEST_BASIC>
1.1567171483619434

> <JCHEM_POLAR_SURFACE_AREA>
96.24000000000001

> <JCHEM_REFRACTIVITY>
46.9446

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[1-(carboximidatoamino)-2-hydroxy-2-oxoethan-2-ium-1-yl]azanylidene

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0334383 (S-ureidoglycine)
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PDB for NP0334383 (S-ureidoglycine)
HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.104  -0.564   0.000  0.00  0.00           C+1
HETATM    3  C   UNK     0       1.897  -1.334   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -0.770  -2.874   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       3.231  -0.564   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       0.564  -0.564   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      -3.437  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.104   0.976   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.897  -2.874   0.000  0.00  0.00           O-1
CONECT    1    2    4    6                                                  
CONECT    2    1    7    8                                                  
CONECT    3    5    6    9                                                  
CONECT    4    1                                                            
CONECT    5    3                                                            
CONECT    6    1    3                                                       
CONECT    7    2                                                            
CONECT    8    2                                                            
CONECT    9    3                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0334383 (S-ureidoglycine)
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SMILES for NP0334383 (S-ureidoglycine)
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INCHI for NP0334383 (S-ureidoglycine)
InChI=1/C3H5N3O3/c4-1(2(7)8)6-3(5)9/h1H,(H,7,8)(H3,5,6,9)/q+1/p-1
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SynonymsNot Available
Chemical FormulaC3H4N3O3
Average Mass130.0830 Da
Monoisotopic Mass130.02527 Da
IUPAC Name[1-(carboximidatoamino)-2-hydroxy-2-oxoethan-2-ium-1-yl]azanylidene
Traditional Name[1-(carboximidatoamino)-2-hydroxy-2-oxoethan-2-ium-1-yl]azanylidene
CAS Registry NumberNot Available
SMILES
InChI Identifier
InChI=1/C3H5N3O3/c4-1(2(7)8)6-3(5)9/h1H,(H,7,8)(H3,5,6,9)/q+1/p-1
InChI KeyAJONJFGFTGGKEX-UHFFFAOYNA-M
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
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-3.9ChemAxon
pKa (Strongest Acidic)-1.2ChemAxon
pKa (Strongest Basic)1.16ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area96.24 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity46.94 m³·mol⁻¹ChemAxon
Polarizability10.29 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 CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Serventi F, Ramazzina I, Lamberto I, Puggioni V, Gatti R, Percudani R: Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria. ACS Chem Biol. 2010 Feb 19;5(2):203-14. doi: 10.1021/cb900248n. [PubMed:20038185  ] 
  2. Yazdanpanah F, Willems LAJ, He H, Hilhorst HWM, Bentsink L: A Role for Allantoate Amidohydrolase (AtAAH) in the Germination of Arabidopsis thaliana Seeds. Plant Cell Physiol. 2022 Sep 15;63(9):1298-1308. doi: 10.1093/pcp/pcac103. [PubMed:35861030  ]