6,7-Dimethyl-8-(1-D-ribityl)lumazine (YMDB00766)

Identification
YMDB IDYMDB00766
Name6,7-Dimethyl-8-(1-D-ribityl)lumazine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description6,7-Dimethyl-8-(1-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. Based on a literature review very few articles have been published on 6,7-Dimethyl-8-(1-D-ribityl)lumazine.
Structure
Thumb
MOLSDFPDBSMILESInChI
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-ribityl)lumazine
  • 6,7-Dimethyl-8-D-ribityllumazine
  • RL-6,7-DiMe
  • 6,7-Dimethyl-8-ribityllumazine, 14C-labeled
  • 6,7-Dimethyl-8-ribityllumazine, (D)-isomer
  • 1-Deoxy-1-(3,4-dihydro-6,7-dimethyl-2,4-dioxo-8(2H)-pteridinyl)-D-ribitol
  • 6,7-Dimethyl-8-(1’-D-ribityl)lumazine
  • 6,7-Dimethylribityllumazine
  • 6,7-Dimethylribolumazine
  • 2,4(1H,3H)-Pteridinedione, 6,7-dimethyl-8-(2,3,4,5-tetrahydroxypentyl)-, [2S-(2R*,3R*,4S*)]-
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)5.97ChemAxon
pKa (Strongest Basic)-1.8ChemAxon
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 uracil → 6,7-Dimethyl-8-(1-D-ribityl)lumazine
6,7-Dimethyl-8-(1-D-ribityl)lumazine → Riboflavin + 5-Amino-6-ribitylamino uracil
KEGG Reactions
5-Amino-6-ribitylamino uracil + 2-Hydroxy-3-oxobutyl phosphate → water + 6,7-Dimethyl-8-(1-D-ribityl)lumazine + phosphate
6,7-Dimethyl-8-(1-D-ribityl)lumazine → Riboflavin + 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 GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0019000000-6a3e2297312b9e0ad05cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a6v-0193000000-af0c9caba180ea68c7d1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0596-2950000000-b94c706faa170396061aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0092000000-952d1c3b4014cc4b1b58JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0aba-3290000000-9b6bebb3cf7d4b5f032aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-6920000000-ece0456a5fd52d62d563JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
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 IDFDB023230
Wikipedia IDNot Available
BioCyc IDDIMETHYL-D-RIBITYL-LUMAZINE

Enzymes

Protein Details
1. 6,7-dimethyl-8-ribityllumazine synthase
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.
Protein Details
2. Riboflavin synthase alpha chain
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.