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Identification
YMDB IDYMDB00766
Name6,7-Dimethyl-8-(1-D-ribityl)lumazine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description6,7-dimethyl-8-(D-ribityl)lumazine, also known as DMDRL or RL-6,7-dime, belongs to the class of organic compounds known as pteridines and derivatives. These are polycyclic aromatic compounds containing a pteridine moiety, which consists of a pyrimidine fused to a pyrazine ring to form pyrimido(4,5-b)pyrazine. 6,7-dimethyl-8-(D-ribityl)lumazine is an extremely weak basic (essentially neutral) compound (based on its pKa). 6,7-dimethyl-8-(D-ribityl)lumazine exists in both E. coli (prokaryote) and yeast (eukaryote). Within yeast, 6,7-dimethyl-8-(D-ribityl)lumazine participates in a number of enzymatic reactions. In particular, 6,7-dimethyl-8-(D-ribityl)lumazine can be biosynthesized from 1-deoxy-L-glycero-tetrulose 4-phosphate and 5-amino-6-ribitylamino uracil; which is catalyzed by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. In addition, 6,7-dimethyl-8-(D-ribityl)lumazine can be converted into riboflavin and 5-amino-6-ribitylamino uracil; which is mediated by the enzyme riboflavin synthase. In yeast, 6,7-dimethyl-8-(D-ribityl)lumazine is involved in the metabolic pathway called the riboflavin metabolism pathway.
Structure
Thumb
Synonyms
  • 1-Deoxy-1-(3,4-dihydro-6,7-dimethyl-2,4-dioxo-8(2H)-pteridinyl)-ribitol
  • 1-deoxy-1-[6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl]-D-ribitol
  • 6,7-dimethyl-8-(1-D-ribityl)lumazine
  • 6,7-Dimethyl-8-(1'-D-ribityl)lumazine
  • 6,7-dimethyl-8-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]pteridine-2,4-dione
  • 6,7-Dimethyl-8-ribityllumazine
  • DMDRL
  • 6,7-Dimethyl-8-D-ribityllumazine
  • RL-6,7-DiMe
  • 6,7-Dimethyl-8-ribityllumazine, 14C-labeled
  • 6,7-Dimethyl-8-ribityllumazine, (D)-isomer
CAS number5118-16-1
WeightAverage: 326.3052
Monoisotopic: 326.122634328
InChI KeySXDXRJZUAJBNFL-XKSSXDPKSA-N
InChIInChI=1S/C13H18N4O6/c1-5-6(2)17(3-7(19)10(21)8(20)4-18)11-9(14-5)12(22)16-13(23)15-11/h7-8,10,18-21H,3-4H2,1-2H3,(H,16,22,23)/t7-,8+,10-/m0/s1
IUPAC Name6,7-dimethyl-8-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]-2,3,4,8-tetrahydropteridine-2,4-dione
Traditional IUPAC Name6,7-dimethyl-8-ribityllumazine
Chemical FormulaC13H18N4O6
SMILESCC1=C(C)N(C[C@H](O)[C@H](O)[C@H](O)CO)C2=NC(=O)NC(=O)C2=N1
Chemical Taxonomy
Description belongs to the class of organic compounds known as pteridines and derivatives. These are polycyclic aromatic compounds containing a pteridine moiety, which consists of a pyrimidine fused to a pyrazine ring to form pyrimido(4,5-b)pyrazine.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPteridines and derivatives
Sub ClassNot Available
Direct ParentPteridines and derivatives
Alternative Parents
Substituents
  • Pteridine
  • Pyrimidone
  • Pyrazine
  • Pyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Lactam
  • Secondary alcohol
  • Polyol
  • Azacycle
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary alcohol
  • Alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogP-3.145PhysProp
Predicted Properties
PropertyValueSource
Water Solubility1.23 g/LALOGPS
logP-1.8ALOGPS
logP-2.7ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)6.97ChemAxon
pKa (Strongest Basic)-1.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area155.05 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity79 m³·mol⁻¹ChemAxon
Polarizability31.25 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Riboflavin metabolismPW002443 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Riboflavin metabolismec00740 Map00740
SMPDB Reactions
2-Hydroxy-3-oxobutyl phosphate + 5-Amino-6-ribitylamino uracil6,7-Dimethyl-8-(1-D-ribityl)lumazine
6,7-Dimethyl-8-(1-D-ribityl)lumazineRiboflavin + 5-Amino-6-ribitylamino uracil
KEGG Reactions
5-Amino-6-ribitylamino uracil + 2-Hydroxy-3-oxobutyl phosphatewater + 6,7-Dimethyl-8-(1-D-ribityl)lumazine + phosphate
6,7-Dimethyl-8-(1-D-ribityl)lumazineRiboflavin + 5-Amino-6-ribitylamino uracil
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0cdi-9083000000-55d05335ecc8773d02f2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a6r-1059000000-456d791c6c92f427e0bbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-4191000000-a369e70429d996cb453fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-056r-3940000000-8631c507779bd52b9fceJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-007o-5090000000-04425d989e04e22e581bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9410000000-a9771614889faa09219bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9400000000-d2188f7f691cd53fb0beJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • 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
  • PLAUT, G. W. (1963). "Studies on the nature of the enzymic conversion of 6,7-dimethyl-8-ribityllumazine to riboflavin." J Biol Chem 238:2225-2243.13944007
  • Bacher, A., Baur, R., Eggers, U., Harders, H. D., Otto, M. K., Schnepple, H. (1980). "Riboflavin synthases of Bacillus subtilis. Purification and properties." J Biol Chem 255:632-637.6766130
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID17601
HMDB IDHMDB03826
Pubchem Compound ID168989
Kegg IDC04332
ChemSpider ID24785452
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDDIMETHYL-D-RIBITYL-LUMAZINE

Enzymes

General function:
Involved in riboflavin biosynthetic process
Specific function:
Condensation of 5-amino-6-(1'-D)-ribityl-amino- 2,4(1H,3H)-pyrimidinedione with L-3,4-dihydroxy-2-butanone 4- phosphate to produce 6,7-dimethyl-8-(1-D-ribityl)lumazine
Gene Name:
RIB4
Uniprot ID:
P50861
Molecular weight:
18555.40039
Reactions
2 6,7-dimethyl-8-(1-D-ribityl)lumazine → riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.
General function:
Involved in riboflavin synthase activity
Specific function:
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
Gene Name:
RIB5
Uniprot ID:
P38145
Molecular weight:
26195.59961
Reactions
2 6,7-dimethyl-8-(1-D-ribityl)lumazine → riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.