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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-07-23 05:44:44 UTC
HMDB IDHMDB0001137
Secondary Accession Numbers
  • HMDB01137
Metabolite Identification
Common NameHydroxymethylbilane
DescriptionHydroxymethylbilane, also known as preuroporphyrinogen, 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. The compound is generated from four molecules of porphobilinogen by the enzyme porphobilinogen deaminase:The enzyme uroporphyrinogen III synthase closes the chain to form a porphyrinogen a class of compounds with the hexahydroporphine macrocycle; specifically, uroporphyrinogen III. The chain starts with a hydroxymethyl group –CH2–OH and ends with an hydrogen, in place of the respective methylene bridges. Hydroxymethylbilane is a weakly acidic compound (based on its pKa). Hydroxymethylbilane exists in all living species, ranging from bacteria to humans. In humans, hydroxymethylbilane is involved in the metabolic disorder called the porphyria variegata (pv) pathway. Outside of the human body, hydroxymethylbilane has been detected, but not quantified in, several different foods, such as other soy products, prickly pears, fennels, sparkleberries, and sugar apples. This could make hydroxymethylbilane a potential biomarker for the consumption of these foods. The other two carbon atoms of each pyrrole cycle are connected to an acetic acid group –CH2–COOH and a propionic acid group –CH2–CH2–COOH, in that order. The name is often abbreviated as HMB.The compound is a substituted bilane, a chain of four pyrrole rings interconnected by methylene bridges –CH2–. In the absence of the enzyme, the compound undergoes spontaneous cyclization and becomes uroporphyrinogen I.
Structure
Data?1563860684
Synonyms
ValueSource
(Hydroxymethyl)bilaneChEBI
3,8,13,18-Tetrakis(carboxymethyl)-5,10,15,22,23,24-hexahydro-19-(hydroxymethyl)-21H-biline-2,7,12,17-tetrapropanoic acidChEBI
3,8,13,18-Tetrakis(carboxymethyl)-5,10,15,22,23,24-hexahydro-19-(hydroxymethyl)-21H-biline-2,7,12,17-tetrapropanoateGenerator
3,8,13,18-Tetrakis(carboxymethyl)-19-(hydroxymethyl)bilane-2,7,12,17-tetrapropanoateHMDB
3,8,13,18-Tetrakis(carboxymethyl)-19-(hydroxymethyl)bilane-2,7,12,17-tetrapropanoic acidHMDB
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]propanoateHMDB
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 acidHMDB
PreuroporphyrinogenHMDB
Chemical FormulaC40H46N4O17
Average Molecular Weight854.8098
Monoisotopic Molecular Weight854.285796066
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 Namehydroxymethylbilane
CAS Registry Number73023-76-4
SMILES
OCC1=C(CC(O)=O)C(CCC(O)=O)=C(CC2=C(CC(O)=O)C(CCC(O)=O)=C(CC3=C(CC(O)=O)C(CCC(O)=O)=C(CC4=C(CC(O)=O)C(CCC(O)=O)=CN4)N3)N2)N1
InChI Identifier
InChI=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)
InChI KeyWDFJYRZCZIUBPR-UHFFFAOYSA-N
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
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
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
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014u-0000000790-0465e102e331b86b0303Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-0000000940-84d7b7307b952e375d11Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-002f-0000000910-4cfaaf03b9bff04a3a7dSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052o-0000000790-1398b69ce01f9c5d047cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-0000000940-b283797ea8328ef028d6Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-1000001930-9e9b406ad31d6bf35cf0Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022446
KNApSAcK IDC00007374
Chemspider ID767
KEGG Compound IDC01024
BioCyc IDNot Available
BiGG ID36648
Wikipedia LinkHydroxymethylbilane
METLIN ID3699
PubChem Compound788
PDB IDNot Available
ChEBI ID16645
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Drager A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO: Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. [PubMed:29457794 ]

Enzymes

General function:
Involved in uroporphyrinogen-III synthase activity
Specific function:
Catalyzes cyclization of the linear tetrapyrrole, hydroxymethylbilane, to the macrocyclic uroporphyrinogen III, the branch point for the various sub-pathways leading to the wide diversity of porphyrins. Porphyrins act as cofactors for a multitude of enzymes that perform a variety of processes within the cell such as methionine synthesis (vitamin B12) or oxygen transport (heme).
Gene Name:
UROS
Uniprot ID:
P10746
Molecular weight:
28627.37
Reactions
Hydroxymethylbilane → Uroporphyrinogen III + Waterdetails
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:
HMBS
Uniprot ID:
P08397
Molecular weight:
39329.74
Reactions
Porphobilinogen + Water → Hydroxymethylbilane + Ammoniadetails