Showing NP-Card for Urea (NP0000591)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2025-02-11 15:41:10 UTC
NP-MRD IDNP0000591
Secondary Accession NumbersNone
Natural Product Identification
Common NameUrea
DescriptionUrea is a highly soluble organic compound formed in the liver from ammonia produced by the deamination of amino acids. It is the principal end product of protein catabolism and constitutes about one half of the total urinary solids. Urea is formed in a cyclic pathway known simply as the urea cycle. In this cycle, amino groups donated by ammonia and L-aspartate are converted to urea. Urea is essentially a waste product; it has no physiological function. It is dissolved in blood (in humans in a concentration of 2.5 - 7.5 Mmol/liter) and excreted by the kidney in the urine. In addition, a small amount of urea is excreted (along with sodium chloride and water) in human sweat. Urea is found to be associated with primary hypomagnesemia, which is an inborn error of metabolism.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000591 (Urea)

  Mrv1652309042000002D          

  4  3  0  0  0  0            999 V2000
    1.3334   -0.6187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957   -0.6187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
M  END
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3D MOL for NP0000591 (Urea)

HMDB0000294
     RDKit          3D
Urea
  8  7  0  0  0  0  0  0  0  0999 V2000
   -1.1986   -0.0447    0.3821 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0214    0.3874   -0.3037 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2215   -0.2582   -0.1226 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1003    1.3713   -1.0899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9476    0.6151    0.6532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3071   -1.0554    0.6168 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4449   -1.0724   -0.7164 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9086    0.0570    0.5805 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  0
  1  5  1  0
  1  6  1  0
  3  7  1  0
  3  8  1  0
M  END
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3D SDF for NP0000591 (Urea)

  Mrv1652309042000002D          

  4  3  0  0  0  0            999 V2000
    1.3334   -0.6187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957   -0.6187    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6187    0.6187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0000591

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(N)=O

> <INCHI_IDENTIFIER>
InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4)

> <INCHI_KEY>
XSQUKJJJFZCRTK-UHFFFAOYSA-N

> <FORMULA>
CH4N2O

> <MOLECULAR_WEIGHT>
60.0553

> <EXACT_MASS>
60.03236276

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
5.102881409078858

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
urea

> <ALOGPS_LOGP>
-1.78

> <JCHEM_LOGP>
-1.3638338616666665

> <ALOGPS_LOGS>
0.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.731965106806726

> <JCHEM_PKA_STRONGEST_BASIC>
-2.3686972237578967

> <JCHEM_POLAR_SURFACE_AREA>
69.11

> <JCHEM_REFRACTIVITY>
13.1426

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.12e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
urea

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0000591 (Urea)

HMDB0000294
     RDKit          3D
Urea
  8  7  0  0  0  0  0  0  0  0999 V2000
   -1.1986   -0.0447    0.3821 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0214    0.3874   -0.3037 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2215   -0.2582   -0.1226 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1003    1.3713   -1.0899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9476    0.6151    0.6532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3071   -1.0554    0.6168 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4449   -1.0724   -0.7164 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9086    0.0570    0.5805 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  0
  1  5  1  0
  1  6  1  0
  3  7  1  0
  3  8  1  0
M  END
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PDB for NP0000591 (Urea)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       2.489  -1.155   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.155  -0.385   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.179  -1.155   0.000  0.00  0.00           N+0
HETATM    4  O   UNK     0       1.155   1.155   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for NP0000591 (Urea)

COMPND    HMDB0000294
HETATM    1  N1  UNL     1      -1.199  -0.045   0.382  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.021   0.387  -0.304  1.00  0.00           C  
HETATM    3  N2  UNL     1       1.222  -0.258  -0.123  1.00  0.00           N  
HETATM    4  O1  UNL     1      -0.100   1.371  -1.090  1.00  0.00           O  
HETATM    5  H1  UNL     1      -1.948   0.615   0.653  1.00  0.00           H  
HETATM    6  H2  UNL     1      -1.307  -1.055   0.617  1.00  0.00           H  
HETATM    7  H3  UNL     1       1.445  -1.072  -0.716  1.00  0.00           H  
HETATM    8  H4  UNL     1       1.909   0.057   0.580  1.00  0.00           H  
CONECT    1    2    5    6
CONECT    2    3    4    4
CONECT    3    7    8
END
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SMILES for NP0000591 (Urea)

NC(N)=O
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INCHI for NP0000591 (Urea)

InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4)
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View in JSmol
Synonyms
Chemical FormulaCH4N2O
Average Mass60.0553 Da
Monoisotopic Mass60.03236 Da
IUPAC Nameurea
Traditional Nameurea
CAS Registry Number57-13-6
SMILES
NC(N)=O
InChI Identifier
InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4)
InChI KeyXSQUKJJJFZCRTK-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-08-03View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)v.dorna83@yahoo.comNot AvailableNot Available2021-07-29View Spectrum
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Bos taurus domesticusKNApSAcK Database
Homo sapiensKNApSAcK Database
Phoma medicaginisKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as ureas. Ureas are compounds containing two amine groups joined by a carbonyl (C=O) functional group.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic carbonic acids and derivatives
Sub ClassUreas
Direct ParentUreas
Alternative Parents
Substituents
  • Urea
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point132 °CNot Available
Boiling Point196.00 to 197.00 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility545 mg/mLNot Available
LogP-2.11Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility412 g/LALOGPS
logP-1.8ALOGPS
logP-1.4ChemAxon
logS0.84ALOGPS
pKa (Strongest Acidic)15.73ChemAxon
pKa (Strongest Basic)-2.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area69.11 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity13.14 m³·mol⁻¹ChemAxon
Polarizability5.1 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000294
DrugBank IDDB03904
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012174
KNApSAcK IDC00007314
Chemspider ID1143
KEGG Compound IDC00086
BioCyc IDUREA
BiGG ID33799
Wikipedia LinkUrea
METLIN ID6
PubChem Compound1176
PDB IDNot Available
ChEBI ID16199
Good Scents IDrw1296171
References
General References