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Identification
YMDB IDYMDB00848
Name(6R)-5,10-methylenetetrahydrofolic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description(6R)-5,10-methylenetetrahydrofolic acid, also known as 5,10-methylene-THF, belongs to the class of organic compounds known as tetrahydrofolic acids. These are heterocyclic compounds based on the 5,6,7,8-tetrahydropteroic acid skeleton conjugated with at least one L-glutamic acid unit (6R)-5,10-methylenetetrahydrofolic acid is a strong basic compound (based on its pKa) (6R)-5,10-methylenetetrahydrofolic acid exists in both E. coli (prokaryote) and yeast (eukaryote).
Structure
Thumb
Synonyms
  • (6R)-5,10-Methylenetetrahydrofolate
  • 5,10-methylene-5,6,7,8-tetrahydrofolate
  • 5,10-Methylene-THF
  • 5,10-Methylenetetrahydrofolate
  • 5,10-methylenetetrahydrofolic acid
  • n5,n10-methylene-5,6,7,8-tetrahydrofolate
  • n5,n10-methylene-tetrahydrofolate
  • (6R)-5,10-Methylenetetrahydrofolic acid
CAS number3432-99-3
WeightAverage: 457.4399
Monoisotopic: 457.170981503
InChI KeyQYNUQALWYRSVHF-OLZOCXBDSA-N
InChIInChI=1S/C20H23N7O6/c21-20-24-16-15(18(31)25-20)27-9-26(8-12(27)7-22-16)11-3-1-10(2-4-11)17(30)23-13(19(32)33)5-6-14(28)29/h1-4,12-13H,5-9H2,(H,23,30)(H,28,29)(H,32,33)(H4,21,22,24,25,31)/t12-,13+/m1/s1
IUPAC Name(2S)-2-({4-[(6aR)-3-amino-1-oxo-1H,2H,5H,6H,6aH,7H,8H,9H-imidazolidino[1,5-f]pteridin-8-yl]phenyl}formamido)pentanedioic acid
Traditional IUPAC Name5,10-Methylene-THF
Chemical FormulaC20H23N7O6
SMILES[H][C@@]12CN(CN1C1=C(NC2)N=C(N)NC1=O)C1=CC=C(C=C1)C(=O)N[C@@H](CCC(O)=O)C(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as tetrahydrofolic acids. These are heterocyclic compounds based on the 5,6,7,8-tetrahydropteroic acid skeleton conjugated with at least one L-glutamic acid unit.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPteridines and derivatives
Sub ClassPterins and derivatives
Direct ParentTetrahydrofolic acids
Alternative Parents
Substituents
  • Tetrahydrofolic acid
  • Glutamic acid or derivatives
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Hippuric acid
  • Hippuric acid or derivatives
  • Phenylimidazolidine
  • Alpha-amino acid or derivatives
  • Benzamide
  • Benzoic acid or derivatives
  • Imidazopyrazine
  • Benzoyl
  • Dialkylarylamine
  • Aniline or substituted anilines
  • Pyrimidone
  • Aminopyrimidine
  • Secondary aliphatic/aromatic amine
  • Benzenoid
  • Pyrimidine
  • Monocyclic benzene moiety
  • Dicarboxylic acid or derivatives
  • Heteroaromatic compound
  • Vinylogous amide
  • Imidazolidine
  • Secondary carboxylic acid amide
  • Amino acid or derivatives
  • Amino acid
  • Carboxamide group
  • Secondary amine
  • Azacycle
  • Carboxylic acid
  • Carboxylic acid derivative
  • Primary amine
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Amine
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.82 g/LALOGPS
logP-0.94ALOGPS
logP-2ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)2.93ChemAxon
pKa (Strongest Basic)4.6ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area189.69 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity123.96 m³·mol⁻¹ChemAxon
Polarizability45.76 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic PropertiesNot Available
SMPDB Pathways
One Carbon Pool by Folate IPW002468 ThumbThumb?image type=greyscaleThumb?image type=simple
Pantothenate and CoA biosynthesisPW002463 ThumbThumb?image type=greyscaleThumb?image type=simple
glycine metabolismPW002398 ThumbThumb?image type=greyscaleThumb?image type=simple
serine metabolismPW002402 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Glycine, serine and threonine metabolismec00260 Map00260
Methane metabolismec00680 Map00680
One carbon pool by folateec00670 Map00670
Pantothenate and CoA biosynthesisec00770 Map00770
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0001900000-be062f23f73faa80d72bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-06ri-1325900000-6420a9d99896c4388b81JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9543000000-544604a154db7e208558JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-0002900000-a88382f350a14348376cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-0329500000-4f7c559817bf6df5a24dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-02w9-1493000000-143061365aaedaec549cJSpectraViewer
References
References:
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Schirch, L. (1982). "Serine hydroxymethyltransferase." Adv Enzymol Relat Areas Mol Biol 53:83-112.7036682
  • Rao, N. A., Talwar, R., Savithri, H. S. (2000). "Molecular organization, catalytic mechanism and function of serine hydroxymethyltransferase--a potential target for cancer chemotherapy." Int J Biochem Cell Biol 32:405-416.10762066
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID1989
HMDB IDNot Available
Pubchem Compound ID439175
Kegg IDC00143
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDMETHYLENE-THF

Enzymes

General function:
Involved in catalytic activity
Specific function:
Interconversion of serine and glycine
Gene Name:
SHM2
Uniprot ID:
P37291
Molecular weight:
52218.0
Reactions
5,10-methylenetetrahydrofolate + glycine + H(2)O → tetrahydrofolate + L-serine.
General function:
Involved in catalytic activity
Specific function:
Interconversion of serine and glycine
Gene Name:
SHM1
Uniprot ID:
P37292
Molecular weight:
53686.0
Reactions
5,10-methylenetetrahydrofolate + glycine + H(2)O → tetrahydrofolate + L-serine.
General function:
Involved in oxidoreductase activity
Specific function:
Lipoamide dehydrogenase is a component of the alpha- ketoacid dehydrogenase complexes. This includes the pyruvate dehydrogenase complex, which catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). Acts also as component of the glycine cleavage system (glycine decarboxylase complex), which catalyzes the degradation of glycine
Gene Name:
LPD1
Uniprot ID:
P09624
Molecular weight:
54009.69922
Reactions
Protein N(6)-(dihydrolipoyl)lysine + NAD(+) → protein N(6)-(lipoyl)lysine + NADH.
General function:
Involved in thymidylate synthase activity
Specific function:
Required for both nuclear and mitochondrial DNA synthesis
Gene Name:
TMP1
Uniprot ID:
P06785
Molecular weight:
35046.89844
Reactions
5,10-methylenetetrahydrofolate + dUMP → dihydrofolate + dTMP.
General function:
Involved in formate-tetrahydrofolate ligase activity
Specific function:
5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH
Gene Name:
MIS1
Uniprot ID:
P09440
Molecular weight:
106216.0
Reactions
5,10-methylenetetrahydrofolate + NADP(+) → 5,10-methenyltetrahydrofolate + NADPH.
5,10-methenyltetrahydrofolate + H(2)O → 10-formyltetrahydrofolate.
ATP + formate + tetrahydrofolate → ADP + phosphate + 10-formyltetrahydrofolate.
General function:
Involved in formate-tetrahydrofolate ligase activity
Specific function:
5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH
Gene Name:
ADE3
Uniprot ID:
P07245
Molecular weight:
102204.0
Reactions
5,10-methylenetetrahydrofolate + NADP(+) → 5,10-methenyltetrahydrofolate + NADPH.
5,10-methenyltetrahydrofolate + H(2)O → 10-formyltetrahydrofolate.
ATP + formate + tetrahydrofolate → ADP + phosphate + 10-formyltetrahydrofolate.
General function:
Involved in 3-methyl-2-oxobutanoate hydroxymethyltransferase activity
Specific function:
5,10-methylenetetrahydrofolate + 3-methyl-2- oxobutanoate + H(2)O = tetrahydrofolate + 2-dehydropantoate
Gene Name:
ECM31
Uniprot ID:
P38122
Molecular weight:
34464.69922
Reactions
5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate + H(2)O → tetrahydrofolate + 2-dehydropantoate.
General function:
Involved in binding
Specific function:
Catalyzes oxidation of cytoplasmic one-carbon units for purine biosynthesis
Gene Name:
MTD1
Uniprot ID:
Q02046
Molecular weight:
36239.30078
Reactions
5,10-methylenetetrahydrofolate + NAD(+) → 5,10-methenyltetrahydrofolate + NADH.
General function:
Involved in methylenetetrahydrofolate reductase (NADPH) activity
Specific function:
5-methyltetrahydrofolate + NAD(P)(+) = 5,10- methylenetetrahydrofolate + NAD(P)H
Gene Name:
MET13
Uniprot ID:
P53128
Molecular weight:
68559.5
Reactions
5-methyltetrahydrofolate + NAD(P)(+) → 5,10-methylenetetrahydrofolate + NAD(P)H.