Showing metabocard for Urea (MMDBc0000093)

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Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:30:07 UTC
Update Date2024-09-27 22:48:47 UTC
Metabolite IDMMDBc0000093
Metabolite 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f53b8a1e1a0>

  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 #<Metabolite:0x00007f53b8a1e1a0>

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 #<Metabolite:0x00007f53b8a1e1a0>

  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>
MMDBc0000093

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f53b8a1e1a0>

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 #<Metabolite:0x00007f53b8a1e1a0>

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 #<Metabolite:0x00007f53b8a1e1a0>

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 #<Metabolite:0x00007f53b8a1e1a0>

NC(N)=O
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INCHI for #<Metabolite:0x00007f53b8a1e1a0>

InChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4)
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Synonyms
Molecular FormulaCH4N2O
Average Mass60.0553
Monoisotopic Mass60.03236276
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