6,7-Dimethyl-8-(1-D-ribityl)lumazine (ECMDB03826) (M2MDB000524)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (801)
Record Information
Version2.0
Creation Date2012-05-31 14:00:20 -0600
Update Date2015-06-03 15:54:32 -0600
Secondary Accession Numbers
  • ECMDB03826
Identification
Name:6,7-Dimethyl-8-(1-D-ribityl)lumazine
Description6,7-Dimethyl-8-(1-D-ribityl)lumazine is an intermediate in riboflavin metabolism. 6,7-Dimethyl-8-(1-D-ribityl)lumazine is the second to last step in the synthesis of ribitol and is converted from 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine via the enzyme riboflavin synthase beta chain. It is then
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-ribityllumazine
  • 6,7-Dimethyl-8-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]pteridine-2,4-dione
  • 6,7D81RbL
  • DMDRL
Chemical Formula:C13H18N4O6
Weight:Average: 326.3052
Monoisotopic: 326.122634328
InChI Key:SXDXRJZUAJBNFL-UHFFFAOYSA-N
InChI:InChI=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)
CAS number:5118-16-1
IUPAC Name:6,7-dimethyl-8-(2,3,4,5-tetrahydroxypentyl)-2,3,4,8-tetrahydropteridine-2,4-dione
Traditional IUPAC Name:6,7-dimethyl-8-(2,3,4,5-tetrahydroxypentyl)-3H-pteridine-2,4-dione
SMILES:CC1=C(C)N(CC(O)C(O)C(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 DescriptorsNot Available
Physical Properties
State:Solid
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Polarizability31.53 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
2 6,7-Dimethyl-8-(1-D-ribityl)lumazine > 5-Amino-6-ribitylamino uracil + Riboflavin
5-Amino-6-ribitylamino uracil + 3,4-Dihydroxy-2-butanone-4-P > 6,7-Dimethyl-8-(1-D-ribityl)lumazine +2 Water + Phosphate
2 6,7-Dimethyl-8-(1-D-ribityl)lumazine <> Riboflavin + 5-Amino-6-ribitylamino uracil
5-Amino-6-ribitylamino uracil + 3,4-Dihydroxy-2-butanone-4-P <> 6,7-Dimethyl-8-(1-D-ribityl)lumazine +2 Water + Phosphate
5-amino-6-(D-ribitylamino)uracil + 3,4-Dihydroxy-2-butanone-4-P > Hydrogen ion + 6,7-Dimethyl-8-(1-D-ribityl)lumazine + Phosphate + Water
Hydrogen ion + 6,7-Dimethyl-8-(1-D-ribityl)lumazine > 5-amino-6-(D-ribitylamino)uracil + Riboflavin
5-Amino-6-ribitylamino uracil + 1-Deoxy-L-glycero-tetrulose 4-phosphate > Water + Phosphate + Hydrogen ion + 6,7-Dimethyl-8-(1-D-ribityl)lumazine + 6,7-Dimethyl-8-(1-D-ribityl)lumazine
6,7-Dimethyl-8-(1-D-ribityl)lumazine + Hydrogen ion + 6,7-Dimethyl-8-(1-D-ribityl)lumazine > Riboflavin + 5-Amino-6-ribitylamino uracil + Riboflavin
2 6,7-Dimethyl-8-(1-D-ribityl)lumazine >5 5-Amino-6-ribitylamino uracil + Riboflavin
SMPDB Pathways:
Flavin biosynthesisPW001971 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0bt9-9031000000-9c630ca6d5cf3abd4fa7View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-0k92-2122193000-4fdebb2ae42933ee8a1eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a6r-1059000000-bb2238e34adbb8c00787View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0bt9-4191000000-b3b1e68b02bd73ae782aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-056r-4940000000-f6a2f6ffebaa7bc97464View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0089-3090000000-c6c55b4bb2cd8266bc7eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9100000000-102fea61448a18c76296View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-d5a60b46dbd297e60a53View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID17601
HMDB IDHMDB03826
Pubchem Compound ID168989
Kegg IDC04332
ChemSpider ID652
Wikipedia IDNot Available
BioCyc IDDIMETHYL-D-RIBITYL-LUMAZINE
EcoCyc IDDIMETHYL-D-RIBITYL-LUMAZINE

Enzymes

Protein Details
1. Riboflavin synthase alpha chain
General function:
Involved in riboflavin synthase activity
Specific function:
Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)- ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2- butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The alpha subunit catalyzes the dismutation of 6,7-dimethyl-8-lumazine to riboflavin and 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)- pyrimidinedione
Gene Name:
ribE
Uniprot ID:
P0AFU8
Molecular weight:
23445
Reactions
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.
Protein Details
2. 6,7-dimethyl-8-ribityllumazine synthase
General function:
Involved in riboflavin biosynthetic process
Specific function:
Riboflavin synthase is a bifunctional enzyme complex catalyzing the formation of riboflavin from 5-amino-6-(1'-D)- ribityl-amino-2,4(1H,3H)-pyrimidinedione and L-3,4-dihydrohy-2- butanone-4-phosphate via 6,7-dimethyl-8-lumazine. The beta subunit catalyzes the condensation of 5-amino-6-(1'-D)-ribityl-amino- 2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4- phosphate yielding 6,7-dimethyl-8-lumazine
Gene Name:
ribH
Uniprot ID:
P61714
Molecular weight:
16156
Reactions
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.