Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 00:59:54 UTC
Update Date2022-03-07 03:17:44 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
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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 Solubility0.56 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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+240.97130932474
DeepCCS[M-H]-239.24730932474
DeepCCS[M-2H]-273.92830932474
DeepCCS[M+Na]+247.82330932474
AllCCS[M+H]+256.332859911
AllCCS[M+H-H2O]+256.432859911
AllCCS[M+NH4]+256.132859911
AllCCS[M+Na]+256.132859911
AllCCS[M-H]-254.332859911
AllCCS[M+Na-2H]-258.732859911
AllCCS[M+HCOO]-263.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5,10-MethylenetetrahydromethanopterinC[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)N36035.7Standard polar33892256
5,10-MethylenetetrahydromethanopterinC[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)N34716.5Standard non polar33892256
5,10-MethylenetetrahydromethanopterinC[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)N36759.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_6) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_7) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_8) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_9) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_10) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_11) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,10-Methylenetetrahydromethanopterin GC-MS (TMS_1_12) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,10-Methylenetetrahydromethanopterin 10V, Positive-QTOFsplash10-00e9-1801012900-abb53c97d149f62ba4522017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,10-Methylenetetrahydromethanopterin 20V, Positive-QTOFsplash10-00ba-3119510400-d5f1f35eebd36ddbccc72017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,10-Methylenetetrahydromethanopterin 40V, Positive-QTOFsplash10-0019-9602010000-00fd56ea443f78d112922017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,10-Methylenetetrahydromethanopterin 10V, Negative-QTOFsplash10-00ll-1119401700-c81357f57713199d18352017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,10-Methylenetetrahydromethanopterin 20V, Negative-QTOFsplash10-004i-3189101300-e8f2c03753d5529d6a0b2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,10-Methylenetetrahydromethanopterin 40V, Negative-QTOFsplash10-004i-9230000000-79a90986e3be7575ee752017-10-06Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
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
MarkerDB IDNot Available
Good Scents IDNot Available
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