5-amino-6-(D-ribitylamino)uracil (ECMDB23016) (M2MDB003406)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2012-10-10 12:12:24 -0600
Update Date2015-06-03 17:25:44 -0600
Secondary Accession Numbers
  • ECMDB23016
Identification
Name:5-amino-6-(D-ribitylamino)uracil
Description5-amino-6-(D-ribitylamino)uracil is involved in the Cofactor riboflavin biosynthesis pathway. It is a substrate of Riboflavin biosynthesis protein RibD that catalyses the following reactions: 2-hydroxy-3-oxobutyl phosphate + 5-amino-6-(D-ribitylamino)uracil => 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(2)O + 1 phosphate and 6,7-dimethyl-8-(1-D-ribityl)lumazine => 5-amino-6-(D-ribitylamino)uracil + riboflavin
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 1-(5-Amino-2,6-dioxo-1,2,3,6-tetrahydro-4-pyrimidinyl)amino-1-deoxy-D-ribitol
  • 4-(1-D-Ribitylamino)-5-amino-2,6-dihydroxypyrimidine
  • 5-amino-2,6-dioxo-4-ribitylaminopyrimidine
  • 5-Amino-6-(1-D-ribitylamino)uracil
  • 5-amino-6-(2S,3S,4R)-2,3,4,5-tetrahydroxypentylamino-1H-pyrimidine-2,4-dione
  • 5-amino-6-ribitylamino-2,4-(1H,3H)pyrimidinedione
  • 5-Amino-6-ribitylaminouracil
  • 5-arpd
  • 6-(1-D-Ribitylamino)-5-amino-2,4-dihydroxypyrimidine
  • 6-(1-D-Ribitylamino)-5-aminouracil
Chemical Formula:C9H16N4O6
Weight:Average: 276.2465
Monoisotopic: 276.106984264
InChI Key:XKQZIXVJVUPORE-RPDRRWSUSA-N
InChI:InChI=1S/C9H16N4O6/c10-5-7(12-9(19)13-8(5)18)11-1-3(15)6(17)4(16)2-14/h3-4,6,14-17H,1-2,10H2,(H3,11,12,13,18,19)/t3-,4+,6-/m0/s1
CAS number:Not Available
IUPAC Name:5-amino-6-{[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]amino}-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name:5-arpd
SMILES:NC1=C(NC[C@H](O)[C@H](O)[C@H](O)CO)NC(=O)NC1=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Aminopyrimidine
  • Pyrimidone
  • Secondary aliphatic/aromatic amine
  • Hydropyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Lactam
  • Urea
  • Secondary alcohol
  • Polyol
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Primary alcohol
  • Alcohol
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Amine
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility14.3 g/LALOGPS
logP-2.4ALOGPS
logP-4.4ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)8.48ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area177.17 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity71.48 m³·mol⁻¹ChemAxon
Polarizability25.82 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0903-9440000000-d4b6a6cff43cc761315fView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_4_38) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ("5-Amino-6-ribitylamino uracil,4TBDMS,#38" TMS) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-056r-1190000000-2514b630f375b2189bfeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-08fu-9750000000-779ce19c1a0e6b0c6932View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9300000000-2f9fc8d8f57a4b3ca8c6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01x0-5490000000-40e672b419cf2a89e723View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9210000000-e4e8a4b406ad4dfd459fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9200000000-0e769fc743b8cee3b542View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0090000000-04a8c31cda1ce3aa2de8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-054o-0490000000-f4be226ba3308c6193eaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4l-9700000000-b24f4f1baf9ef6a124b9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-056r-0290000000-dbb8670827f983a8ba0fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-052g-2900000000-2170e047feac10873419View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9400000000-c7d08326dc254630e183View in MoNA
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
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID15934
HMDB IDHMDB0011106
Pubchem Compound ID193516
Kegg IDC04732
ChemSpider ID167930
Wikipedia IDNot Available
BioCyc IDNot Available

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.