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Identification
YMDB IDYMDB00145
NameHydroxymethylbilane
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionHydroxymethylbilane is the precursor to uroporphyrinogen-III in tetrapyrrole biosynthesis pathway which starts with the formation of 5-aminolevulinic acid from glycine and succinyl CoA by the enzyme ALA synthase. Uroporphyrinogen-III is a major branch point that leads to biosynthesis of different tetrapyrrole compounds (e.g. porphyrins). Tetrapyrroles usually function as a metal-binding cofactor in many important enzymes, proteins and pigments, such as heme, chlorophyll, cobalamine, siroheme, and cofator F430. [Biocyc PWY-5189]
Structure
Thumb
Synonyms
  • 3-[2-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-3-yl]propanoate
  • 3-[2-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-5-[[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl]-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-3-yl]propanoic acid
  • 3,8,13,18-tetrakis(carboxymethyl)-19-(hydroxymethyl)bilane-2,7,12,17-tetrapropanoate
  • 3,8,13,18-tetrakis(carboxymethyl)-19-(hydroxymethyl)bilane-2,7,12,17-tetrapropanoic acid
  • 3,8,13,18-tetrakis(carboxymethyl)-5,10,15,22,23,24-hexahydro-19-(hydroxymethyl)-21H-Biline-2,7,12,17-tetrapropanoate
  • 3,8,13,18-tetrakis(carboxymethyl)-5,10,15,22,23,24-hexahydro-19-(hydroxymethyl)-21H-Biline-2,7,12,17-tetrapropanoic acid
  • hydroxymethylbilane
  • Preuroporphyrinogen
  • (Hydroxymethyl)bilane
CAS number73023-76-4
WeightAverage: 854.8098
Monoisotopic: 854.285796066
InChI KeyWDFJYRZCZIUBPR-UHFFFAOYSA-N
InChIInChI=1S/C40H46N4O17/c45-17-32-25(12-40(60)61)21(4-8-36(52)53)29(44-32)15-31-24(11-39(58)59)20(3-7-35(50)51)28(43-31)14-30-23(10-38(56)57)19(2-6-34(48)49)27(42-30)13-26-22(9-37(54)55)18(16-41-26)1-5-33(46)47/h16,41-45H,1-15,17H2,(H,46,47)(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)
IUPAC Name3-(2-{[4-(2-carboxyethyl)-5-{[4-(2-carboxyethyl)-5-{[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-3-yl)propanoic acid
Traditional IUPAC Namehydroxymethylbilane
Chemical FormulaC40H46N4O17
SMILES[H]OC(=O)C([H])([H])C1=C(N([H])C([H])=C1C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])C1=C(C(=C(N1[H])C([H])([H])C1=C(C(=C(N1[H])C([H])([H])C1=C(C(=C(N1[H])C([H])([H])O[H])C([H])([H])C(=O)O[H])C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])C(=O)O[H])C([H])([H])C([H])([H])C(=O)O[H])C([H])([H])C(=O)O[H])C([H])([H])C([H])([H])C(=O)O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as tetrapyrroles and derivatives. These are polycyclic aromatic compounds containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassNot Available
Direct ParentTetrapyrroles and derivatives
Alternative Parents
Substituents
  • Tetrapyrrole skeleton
  • Substituted pyrrole
  • Pyrrole
  • Heteroaromatic compound
  • Azacycle
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Aromatic alcohol
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Organic oxide
  • Organopnictogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.032 g/LALOGPS
logP0.53ALOGPS
logP0.97ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)3.25ChemAxon
Physiological Charge-8ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area381.79 ŲChemAxon
Rotatable Bond Count27ChemAxon
Refractivity209.92 m³·mol⁻¹ChemAxon
Polarizability85.68 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Porphyrin MetabolismPW002462 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Porphyrin and chlorophyll metabolismec00860 Map00860
SMPDB Reactions
Porphobilinogen + waterHydroxymethylbilane + Ammonia
HydroxymethylbilaneUroporphyrinogen III + water
KEGG Reactions
Porphobilinogen + waterAmmonium + Hydroxymethylbilane
HydroxymethylbilaneUroporphyrinogen III + water
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014u-0000000790-0465e102e331b86b0303JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-0000000940-84d7b7307b952e375d11JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-002f-0000000910-4cfaaf03b9bff04a3a7dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052o-0000000790-1398b69ce01f9c5d047cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-0000000940-b283797ea8328ef028d6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-1000001930-9e9b406ad31d6bf35cf0JSpectraViewer
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
  • Chelstowska, A., Rytka, J. (1993). "[Biosynthesis of heme in yeast Saccharomyces cerevisiae]." Postepy Biochem 39:173-185.8234090
  • Hoffman, M., Gora, M., Rytka, J. (2003). "Identification of rate-limiting steps in yeast heme biosynthesis." Biochem Biophys Res Commun 310:1247-1253.14559249
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID16645
HMDB IDHMDB01137
Pubchem Compound ID788
Kegg IDC01024
ChemSpider ID767
FOODB IDFDB022446
WikipediaHydroxymethylbilane
BioCyc IDHYDROXYMETHYLBILANE

Enzymes

General function:
Involved in hydroxymethylbilane synthase activity
Specific function:
Tetrapolymerization of the monopyrrole PBG into the hydroxymethylbilane pre-uroporphyrinogen in several discrete steps
Gene Name:
HEM3
Uniprot ID:
P28789
Molecular weight:
36674.19922
Reactions
4 porphobilinogen + H(2)O → hydroxymethylbilane + 4 NH(3).
General function:
Involved in uroporphyrinogen-III synthase activity
Specific function:
Catalyzes cyclization of the linear tetrapyrrole, hydroxymethylbilane, to the macrocyclic uroporphyrinogen III
Gene Name:
HEM4
Uniprot ID:
P06174
Molecular weight:
30911.30078
Reactions
Hydroxymethylbilane → uroporphyrinogen III + H(2)O.