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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2013-05-17 00:59:54 UTC
Update Date2019-07-23 07:14:15 UTC
HMDB IDHMDB0060401
Secondary Accession Numbers
  • HMDB60401
Metabolite Identification
Common Name5,10-Methylenetetrahydromethanopterin
Description5,10-Methylenetetrahydromethanopterin belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. These are lipids containing a glycosyl moiety (one or several units) linked to the hydroxyl group of a fatty alcohol. 5,10-Methylenetetrahydromethanopterin is an extremely strong basic compound (based on its pKa). 5,10-Methylenetetrahydromethanopterin exists in all living organisms, ranging from bacteria to humans.
Structure
Data?1563866055
Synonyms
ValueSource
N5,N10-MethylenetetrahydromethanopterinChEBI
Chemical FormulaC31H45N6O16P
Average Molecular Weight788.6934
Monoisotopic Molecular Weight788.262965934
IUPAC Name(2S)-2-[({[(2R,3S,4R,5S)-5-{[(2R,3S,4S)-5-{4-[(6S,6aR,7R)-1-hydroxy-3-imino-6,7-dimethyl-3H,4H,5H,6H,6aH,7H,8H,9H-imidazolidino[1,5-f]pteridin-8-yl]phenyl}-2,3,4-trihydroxypentyl]oxy}-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]pentanedioic acid
Traditional Name(2S)-2-({[(2R,3S,4R,5S)-5-{[(2R,3S,4S)-5-{4-[(6S,6aR,7R)-1-hydroxy-3-imino-6,7-dimethyl-4H,5H,6H,6aH,7H,9H-imidazolidino[1,5-f]pteridin-8-yl]phenyl}-2,3,4-trihydroxypentyl]oxy}-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy)pentanedioic acid
CAS Registry NumberNot Available
SMILES
C[C@@H]1[C@H]2[C@H](C)NC3=C(N2CN1C1=CC=C(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]2O[C@H](COP(O)(=O)O[C@@H](CCC(O)=O)C(O)=O)[C@@H](O)[C@H]2O)C=C1)C(O)=NC(=N)N3
InChI Identifier
InChI=1S/C31H45N6O16P/c1-13-22-14(2)36(12-37(22)23-27(33-13)34-31(32)35-28(23)45)16-5-3-15(4-6-16)9-17(38)24(42)18(39)10-50-30-26(44)25(43)20(52-30)11-51-54(48,49)53-19(29(46)47)7-8-21(40)41/h3-6,13-14,17-20,22,24-26,30,38-39,42-44H,7-12H2,1-2H3,(H,40,41)(H,46,47)(H,48,49)(H4,32,33,34,35,45)/t13-,14+,17-,18+,19-,20+,22+,24-,25+,26+,30-/m0/s1
InChI KeyGBMIGEWJAPFSQI-CAFBYHECSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Halopyrimidine
  • Pyrimidone
  • Aryl fluoride
  • Aryl halide
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Lactam
  • Urea
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organooxygen compound
  • Organonitrogen compound
  • Organofluoride
  • Organohalogen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary alcohol
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Not Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.56 g/LALOGPS
logP-1ALOGPS
logP-3.7ChemAxon
logS-3.2ALOGPS
pKa (Strongest Acidic)-1.5ChemAxon
pKa (Strongest Basic)15ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area336.95 ŲChemAxon
Rotatable Bond Count17ChemAxon
Refractivity200.9 m³·mol⁻¹ChemAxon
Polarizability77.34 ųChemAxon
Number of Rings5ChemAxon
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, Positivesplash10-00e9-1801012900-abb53c97d149f62ba452Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00ba-3119510400-d5f1f35eebd36ddbccc7Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0019-9602010000-00fd56ea443f78d11292Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00ll-1119401700-c81357f57713199d1835Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-3189101300-e8f2c03753d5529d6a0bSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9230000000-79a90986e3be7575ee75Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC04377
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440314
PDB IDNot Available
ChEBI ID16568
Food Biomarker OntologyNot Available
VMH IDMTETHNPN
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Enzymes

General function:
Involved in catalytic activity
Specific function:
Contributes to the de novo mitochondrial thymidylate biosynthesis pathway. Required to prevent uracil accumulation in mtDNA. Interconversion of serine and glycine. Associates with mitochondrial DNA.
Gene Name:
SHMT2
Uniprot ID:
P34897
Molecular weight:
54862.125
Reactions
L-Serine + 5,6,7,8-Tetrahydromethanopterin → 5,10-Methylenetetrahydromethanopterin + Glycine + Waterdetails
General function:
Involved in catalytic activity
Specific function:
Interconversion of serine and glycine.
Gene Name:
SHMT1
Uniprot ID:
P34896
Molecular weight:
53082.18
Reactions
L-Serine + 5,6,7,8-Tetrahydromethanopterin → 5,10-Methylenetetrahydromethanopterin + Glycine + Waterdetails