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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-07-21 15:10:08 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 congenital erythropoietic porphyria (cep) or gunther disease pathway. Outside of the human body, Hydroxymethylbilane has been detected, but not quantified in, several different foods, such as garden tomato, chinese cabbages, persian limes, rosemaries, and sacred lotus. This could make hydroxymethylbilane a potential biomarker for the consumption of these foods. The name is often abbreviated as HMB.The compound is a substituted bilane, a chain of four pyrrole rings interconnected by methylene bridges −CH2−. 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. In the absence of the enzyme, the compound undergoes spontaneous cyclization and becomes uroporphyrinogen I.
Structure
Data?1595344208
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
3,8,13,18-Tetrakis(carboxymethyl)-5,10,15,22,23,24-hexahydro-19-(hydroxymethyl)-21H-biline-2,7,12,17-tetrapropionic acidHMDB
HydroxymethylbilaneHMDB
Chemical FormulaC40H46N4O17
Average Molecular Weight854.8098
Monoisotopic Molecular Weight854.285796066
IUPAC Name3-(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 Name3-(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
CAS Registry Number71861-60-4
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
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular 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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+284.2332859911
AllCCS[M-H]-285.64832859911
DeepCCS[M+H]+271.18230932474
DeepCCS[M-H]-269.28630932474
DeepCCS[M-2H]-303.04330932474
DeepCCS[M+Na]+276.97230932474
AllCCS[M+H]+284.232859911
AllCCS[M+H-H2O]+284.132859911
AllCCS[M+NH4]+284.332859911
AllCCS[M+Na]+284.332859911
AllCCS[M-H]-285.632859911
AllCCS[M+Na-2H]-291.532859911
AllCCS[M+HCOO]-297.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
HydroxymethylbilaneOCC1=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)N17356.3Standard polar33892256
HydroxymethylbilaneOCC1=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)N15103.0Standard non polar33892256
HydroxymethylbilaneOCC1=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)N17680.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
MSMass Spectrum (Electron Ionization)Not Available2022-08-06Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 10V, Positive-QTOFsplash10-014u-0000000790-0465e102e331b86b03032015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 20V, Positive-QTOFsplash10-0006-0000000940-84d7b7307b952e375d112015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 40V, Positive-QTOFsplash10-002f-0000000910-4cfaaf03b9bff04a3a7d2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 10V, Negative-QTOFsplash10-052o-0000000790-1398b69ce01f9c5d047c2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 20V, Negative-QTOFsplash10-0006-0000000940-b283797ea8328ef028d62015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 40V, Negative-QTOFsplash10-052f-1000001930-9e9b406ad31d6bf35cf02015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 10V, Negative-QTOFsplash10-01ox-0000000900-be1376bf8d447c596ca62021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 20V, Negative-QTOFsplash10-03xu-0000000900-a2d6c191927cc76b8b5b2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 40V, Negative-QTOFsplash10-01w4-0100020900-38c7a5fb40b79705b4202021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 10V, Positive-QTOFsplash10-000f-0000000960-014b54cbe7492f0da1082021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 20V, Positive-QTOFsplash10-0007-0000000900-ab9d5ede3ef2151c6c9e2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Hydroxymethylbilane 40V, Positive-QTOFsplash10-01oy-1110001910-bfe90c78d3e5c8f938252021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)2022-08-20Wishart LabView Spectrum
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
FooDB IDFDB022446
KNApSAcK IDC00007374
Chemspider ID767
KEGG Compound IDC01024
BioCyc IDHYDROXYMETHYLBILANE
BiGG ID36648
Wikipedia LinkHydroxymethylbilane
METLIN ID3699
PubChem Compound788
PDB IDNot Available
ChEBI ID16645
Food Biomarker OntologyNot Available
VMH IDHMBIL
MarkerDB IDNot Available
Good Scents 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