Hydroxymethylbilane (ECMDB01137) (M2MDB000271)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (794)
Record Information
Version2.0
Creation Date2012-05-31 13:46:11 -0600
Update Date2015-06-03 15:53:46 -0600
Secondary Accession Numbers
  • ECMDB01137
Identification
Name:Hydroxymethylbilane
DescriptionHydroxymethylbilane is a molecule involved in the metabolism of porphyrin. In the third step, it is generated by the enzyme porphobilinogen deaminase , and in the next step the enzyme uroporphyrinogen I synthase converts it into uroporphyrinogen I. -- Wikipedia
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 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
  • 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
  • HMB
  • Hydroxymethylbilane
  • Preuroporphyrinogen
Chemical Formula:C40H46N4O17
Weight:Average: 854.8098
Monoisotopic: 854.285796066
InChI Key:WDFJYRZCZIUBPR-UHFFFAOYSA-N
InChI: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)
CAS number:73023-76-4
IUPAC Name:3-(5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-2-yl]methyl}-2-{[4-(2-carboxyethyl)-5-{[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl)propanoic acid
Traditional IUPAC Name:3-(5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-(hydroxymethyl)-1H-pyrrol-2-yl]methyl}-2-{[4-(2-carboxyethyl)-5-{[4-(2-carboxyethyl)-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-3-(carboxymethyl)-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl)propanoic acid
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
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
State:Solid
Charge:-8
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Reactions:
Hydroxymethylbilane <> Water + Uroporphyrinogen III
Water + 4 Porphobilinogen > Hydroxymethylbilane +4 Ammonium
4 Porphobilinogen + Water <> Hydroxymethylbilane +4 Ammonia
Water + Porphobilinogen <> Hydrogen ion + Ammonia + Hydroxymethylbilane
4 Porphobilinogen + Water > Hydroxymethylbilane +4 Ammonia
Hydroxymethylbilane > Uroporphyrinogen III + Water
Hydroxymethylbilane <> Water + Uroporphyrinogen III
4 Porphobilinogen + Water <> Hydroxymethylbilane +4 Ammonia
4 Porphobilinogen + Water <> Hydroxymethylbilane +4 Ammonia
SMPDB Pathways:
Porphyrin metabolismPW000936 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014u-0000000790-0465e102e331b86b0303View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-0000000940-84d7b7307b952e375d11View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-002f-0000000910-4cfaaf03b9bff04a3a7dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052o-0000000790-1398b69ce01f9c5d047cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-0000000940-b283797ea8328ef028d6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-1000001930-9e9b406ad31d6bf35cf0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01ox-0000000900-be1376bf8d447c596ca6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03xu-0000000900-a2d6c191927cc76b8b5bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-01w4-0100020900-38c7a5fb40b79705b420View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000f-0000000960-014b54cbe7492f0da108View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0007-0000000900-ab9d5ede3ef2151c6c9eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01oy-1110001910-bfe90c78d3e5c8f93825View in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16645
HMDB IDHMDB01137
Pubchem Compound ID788
Kegg IDC01024
ChemSpider ID767
WikipediaHydroxymethylbilane
BioCyc IDHYDROXYMETHYLBILANE
EcoCyc IDHYDROXYMETHYLBILANE

Enzymes

Protein Details
1. Porphobilinogen deaminase
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:
hemC
Uniprot ID:
P06983
Molecular weight:
33851
Reactions
4 porphobilinogen + H(2)O = hydroxymethylbilane + 4 NH(3).
Protein Details
2. Uroporphyrinogen-III synthase
General function:
Involved in uroporphyrinogen-III synthase activity
Specific function:
Catalyzes cyclization of the linear tetrapyrrole, hydroxymethylbilane, to the macrocyclic uroporphyrinogen III
Gene Name:
hemD
Uniprot ID:
P09126
Molecular weight:
27798
Reactions
Hydroxymethylbilane = uroporphyrinogen III + H(2)O.