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Urea (YMDB00003)

Identification
YMDB IDYMDB00003
NameUrea
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionUrea, also known as ur or carbamide, 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. Urea is an extremely weak basic (essentially neutral) compound (based on its pKa). Urea exists in all living species, ranging from bacteria to humans. Urea is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • Alphadrate
  • Aqua care HP
  • Aquacare HP
  • ARF
  • b-I-K
  • Basodexan
  • beta-I-K
  • Bromisovalum
  • Bubber shet
  • Calmurid
  • Calmurid HC
  • Carbaderm
  • Carbamide
  • Carbamide resin
  • Carbamimic acid
  • Carbamimidic acid
  • Carbonyl diamide
  • Carbonyl diamine
  • Carbonyldiamide
  • Carbonyldiamine
  • Carmol
  • Carmol HC
  • e927b
  • H2NC(O)NH2
  • Harnstoff
  • Helicosol
  • Hyanit
  • Isourea
  • Karbamid
  • Keratinamin
  • Keratinamin kowa
  • Mocovina
  • Onychomal
  • Panafil
  • Pastaron
  • U-cort
  • ur
  • URE
  • Urea
  • Urea perhydrate
  • Ureaphil
  • Uree
  • Ureophil
  • Urepeal
  • Urevert
  • Varioform II
  • 1728
CAS number57-13-6
WeightAverage: 60.0553
Monoisotopic: 60.03236276
InChI KeyXSQUKJJJFZCRTK-UHFFFAOYSA-N
InChIInChI=1S/CH4N2O/c2-1(3)4/h(H4,2,3,4)
IUPAC Nameurea
Traditional IUPAC Nameurea
Chemical FormulaCH4N2O
SMILES[H]N([H])C(=O)N([H])[H]
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
Charge0
Melting point132 °C
Experimental Properties
PropertyValueReference
Water Solubility545 mg/mL at 25 oC [YALKOWSKY,SH (1989)]PhysProp
LogP-2.11 [HANSCH,C ET AL. (1995)]PhysProp
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Glutamate MetabolismPW002376 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Arginine and proline metabolismec00330 Map00330
Purine metabolismec00230 Map00230
Pyrimidine metabolismec00240 Map00240
SMPDB Reactions
L-Arginine + water → Ornithine + Urea
KEGG Reactions
Allantoic acid + water ↔ Urea + Ureidoglycolic acid
L-Arginine + water → Ornithine + Urea
Carbonic acid + Adenosine triphosphate + Urea ↔ phosphate + hydron + ADP + urea-1-carboxylic acid
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0002-0900000000-234545ed5860ba077237JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0079-3900000000-0ef80e5f5cd9dd6bd213JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-02tc-9000000000-d69da17ffbb84fb6bdcaJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0002-0900000000-234545ed5860ba077237JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0079-3900000000-0ef80e5f5cd9dd6bd213JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0002-1900000000-d805e3019d86aaf9fec0JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9000000000-400d59bf59b857bd7c06JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-9000000000-8f09c5d6f5e002dfa52eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-03dl-9000000000-3d983e9f9115869f55c8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-001i-9000000000-9404d66c59d266164c23JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-03di-9000000000-828ab6c68e3a46ccbd88JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-01ot-9000000000-91554974873c3217dc93JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 0V, Positivesplash10-03di-9000000000-9d3431eab9093f365e2bJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-9000000000-4bdf0d3bd74007ba840aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9000000000-7184b34bac3a316d9feaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-37fd015e8c20febde95aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-9000000000-2fc4ec950c571662bb31JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4l-9000000000-3443c9c73d9a3f03e398JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-11d83d6bda76c25ec73fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052f-9000000000-39cd266ec67397ab213fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9000000000-90726b17dc36e29c5299JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-90726b17dc36e29c5299JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01ox-9000000000-95a1106bd10162ddd326JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-9000000000-b759ce75f0e73d2777dbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-fd9f25340762315b4515JSpectraViewer
MSMass Spectrum (Electron Ionization)splash10-02tc-9000000000-871569893ccfa5dd5395JSpectraViewer | MoNA
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Navarathna, D. H., Harris, S. D., Roberts, D. D., Nickerson, K. W. (2010). "Evolutionary aspects of urea utilization by fungi." FEMS Yeast Res 10:209-213.20100286
  • Eisenstein, E., Osborne, J. C. Jr, Chaiken, I. M., Hensley, P. (1984). "Purification and characterization of ornithine transcarbamoylase from Saccharomyces cerevisiae." J Biol Chem 259:5139-5145.6370999
  • Lawther, R. P., Riemer, E., Chojnacki, B., Cooper, T. G. (1974). "Clustering of the genes for allantoin degradation in Saccharomyces cerevisiae." J Bacteriol 119:461-468.4604238
Synthesis Reference:Leuthardt, F.; Glasson, B. Biological synthesis of urea. Verhandl. Ver. schweiz. Physiol. (1942), 21 25-7.
External Links:
ResourceLink
CHEBI ID16199
HMDB IDHMDB00294
Pubchem Compound ID1176
Kegg IDC00086
ChemSpider ID1143
FOODB IDFDB012174
WikipediaUrea
BioCyc IDUREA

Enzymes

Protein Details
1. Urea amidolyase
General function:
Involved in carbon-nitrogen ligase activity, with glutamine as amido-N-donor
Specific function:
Hydrolysis of urea to ammonia and CO(2)
Gene Name:
DUR1
Uniprot ID:
P32528
Molecular weight:
201830.0
Reactions
ATP + urea + HCO(3)(-) → ADP + phosphate + urea-1-carboxylate.
Urea-1-carboxylate + H(2)O → 2 CO(2) + 2 NH(3).
Protein Details
2. Allantoicase
General function:
Involved in allantoicase activity
Specific function:
Utilization of purines as secondary nitrogen sources, when primary sources are limiting
Gene Name:
DAL2
Uniprot ID:
P25335
Molecular weight:
38713.5
Reactions
Allantoate + H(2)O → (S)-ureidoglycolate + urea.
Protein Details
3. Arginase
General function:
Involved in arginase activity
Specific function:
L-arginine + H(2)O = L-ornithine + urea
Gene Name:
CAR1
Uniprot ID:
P00812
Molecular weight:
35661.60156
Reactions
L-arginine + H(2)O → L-ornithine + urea.

Transporters

Protein Details
1. Urea active transporter
General function:
Involved in transporter activity
Specific function:
Required for active transport of urea
Gene Name:
DUR3
Uniprot ID:
P33413
Molecular weight:
80616.10156