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Showing NP-Card for Ureidoglycine (NP0054976)

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Record Information
Version1.0
Created at2022-04-28 01:10:00 UTC
Updated at2022-04-28 01:10:00 UTC
NP-MRD IDNP0054976
Secondary Accession NumbersNone
Natural Product Identification
Common NameUreidoglycine
Description Ureidoglycine is found in Escherichia coli. It was first documented in 2010 (PMID: 20038185).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0054976 (Ureidoglycine)

 
  Mrv1652303082008462D          
 
  9  8  0  0  1  0            999 V2000
   12.7176   -9.3501    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.4340   -9.7615    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.0081   -9.7615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1504   -9.3501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8634   -9.7615    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.1504   -8.5241    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2897   -9.3483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0096  -10.5947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7176   -8.5251    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  2  0  0  0  0
  1  9  1  1  0  0  0
M  END
Download

3D MOL for NP0054976 (Ureidoglycine)

     RDKit          3D

 16 15  0  0  0  0  0  0  0  0999 V2000
    2.8280    0.1160   -0.1370 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4825    0.2332    0.2940 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2359    1.1342    1.1013 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4801   -0.6630   -0.2338 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9144   -0.5733    0.0997 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8678   -0.9614   -0.8506 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2007    0.8036    0.7215 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3896    0.9798    1.9130 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2247    1.8736   -0.1748 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3126    0.8892   -0.5645 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2889   -0.8407   -0.0025 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7579   -1.4932   -0.8353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9995   -1.2162    1.0715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4883   -1.1243   -1.8166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4358   -1.7763   -0.5011 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8652    2.6188   -0.0849 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  1  1  0
  2  3  2  0
  5  7  1  0
  7  9  1  0
  7  8  2  0
  6 14  1  0
  6 15  1  0
  5 13  1  1
  4 12  1  0
  1 10  1  0
  1 11  1  0
  9 16  1  0
M  END
Download

3D SDF for NP0054976 (Ureidoglycine)

 
  Mrv1652303082008462D          
 
  9  8  0  0  1  0            999 V2000
   12.7176   -9.3501    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.4340   -9.7615    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.0081   -9.7615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1504   -9.3501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8634   -9.7615    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.1504   -8.5241    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2897   -9.3483    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0096  -10.5947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.7176   -8.5251    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  2  0  0  0  0
  1  9  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0054976

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H7N3O3/c4-1(2(7)8)6-3(5)9/h1H,4H2,(H,7,8)(H3,5,6,9)/t1-/m0/s1

> <INCHI_KEY>
VTFWFHCECSOPSX-SFOWXEAESA-N

> <FORMULA>
C3H7N3O3

> <MOLECULAR_WEIGHT>
133.106

> <EXACT_MASS>
133.048741105

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
11.209566683612945

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-2-(carbamoylamino)acetic acid

> <ALOGPS_LOGP>
-3.34

> <JCHEM_LOGP>
-4.313380466949529

> <ALOGPS_LOGS>
-0.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.459762547615679

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4288448573330026

> <JCHEM_PKA_STRONGEST_BASIC>
7.411829551700666

> <JCHEM_POLAR_SURFACE_AREA>
118.43999999999998

> <JCHEM_REFRACTIVITY>
26.9798

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.82e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-2-ureidoglycine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0054976 (Ureidoglycine)

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PDB for NP0054976 (Ureidoglycine)
HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0      23.740 -17.454   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      25.077 -18.221   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      22.415 -18.221   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      26.414 -17.454   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      27.745 -18.221   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0      26.414 -15.912   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      21.074 -17.450   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      22.418 -19.777   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      23.740 -15.914   0.000  0.00  0.00           N+0
CONECT    1    2    3    9                                                  
CONECT    2    1    4                                                       
CONECT    3    1    7    8                                                  
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    3                                                            
CONECT    8    3                                                            
CONECT    9    1                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0054976 (Ureidoglycine)
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SMILES for NP0054976 (Ureidoglycine)
N[C@@H](NC(N)=O)C(O)=O
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INCHI for NP0054976 (Ureidoglycine)
InChI=1S/C3H7N3O3/c4-1(2(7)8)6-3(5)9/h1H,4H2,(H,7,8)(H3,5,6,9)/t1-/m0/s1
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View in JSmol
Synonyms
ValueSource
(2S)-Amino(carbamoylamino)acetic acidChEBI
(2S)-Amino(carbamoylamino)ethanoic acidChEBI
(2S)-UreidoglycineChEBI
(2S)-Amino(carbamoylamino)acetateGenerator
(2S)-Amino(carbamoylamino)ethanoateGenerator
Chemical FormulaC3H7N3O3
Average Mass133.1060 Da
Monoisotopic Mass133.04874 Da
IUPAC Name(2S)-2-amino-2-(carbamoylamino)acetic acid
Traditional Name(S)-2-ureidoglycine
CAS Registry NumberNot Available
SMILES
N[C@@H](NC(N)=O)C(O)=O
InChI Identifier
InChI=1S/C3H7N3O3/c4-1(2(7)8)6-3(5)9/h1H,4H2,(H,7,8)(H3,5,6,9)/t1-/m0/s1
InChI KeyVTFWFHCECSOPSX-SFOWXEAESA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Escherichia coliBacteria
Chemical Taxonomy
Description Belongs to the class of organic 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.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentN-carbamoyl-alpha amino acids  
Alternative Parents
Substituents
  • N-carbamoyl-alpha-amino acid
    • 

  • Urea
    • 

  • Carbonic acid derivative
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Carbonyl group
    • 

  • 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-3.3ALOGPS
logP-4.3ChemAxon
logS-0.36ALOGPS
pKa (Strongest Acidic)1.43ChemAxon
pKa (Strongest Basic)7.41ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area118.44 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity26.98 m³·mol⁻¹ChemAxon
Polarizability11.21 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 IDC00007467  
Chemspider IDNot Available
KEGG Compound IDC02091  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound45479615  
PDB IDNot Available
ChEBI ID59945  
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  ]