ECMDB: 5-Amino-6-ribitylamino uracil (ECMDB04145) (M2MDB000635)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)XML

Proteins (843)

Record Information

Version

2.0

Creation Date

2012-05-31 14:06:25 -0600

Update Date

2015-06-03 15:54:47 -0600

Secondary Accession Numbers

ECMDB04145

Identification

Name:

5-Amino-6-ribitylamino uracil

Description

5-Amino-6-ribitylamino uracil is an intermediate in riboflavin metabolism. It is converted from 5-Amino-6-(5'-phosphoribitylamino)uracil via dephosphorylation by the enzyme phosphohistidine phosphatase 1 (EC 3.1.3.-). (HMDB, KEGG)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

1-[(5-Amino-2,6-dihydroxypyrimidin-4-yl)amino]-1-deoxy-D-ribitol
1-[(5-Amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-1-deoxy-D-ribitol
4-(1-D-Ribitylamino)-5-amino-2,6 dihydroxypyrimidine
4-(1-D-Ribitylamino)-5-amino-2,6-dihydroxypyrimidine
4-(1-D-Ribitylamino)-5-aminouracil
5-Amino-6-(2,3,4,5-tetrahydroxypentylamino)-1H-pyrimidine-2,4-dione
5A6RbA2,4PD
6-Ribitylamino-5-aminouracil

Chemical Formula:

C₉H₁₆N₄O₆

Weight:

Average: 276.2465
Monoisotopic: 276.106984264

InChI Key:

XKQZIXVJVUPORE-UHFFFAOYSA-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)

CAS number:

Not Available

IUPAC Name:

5-amino-6-[(2,3,4,5-tetrahydroxypentyl)amino]-1,2,3,4-tetrahydropyrimidine-2,4-dione

Traditional IUPAC Name:

5-amino-6-[(2,3,4,5-tetrahydroxypentyl)amino]-1,3-dihydropyrimidine-2,4-dione

SMILES:

NC1=C(NCC(O)C(O)C(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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

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 Framework

Aromatic heteromonocyclic compounds

External Descriptors

a small molecule (AMINO-RIBOSYLAMINO-1H-3H-PYR-DIONE )

Physical Properties

State:

Solid

Charge:

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	14.3 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-4.4	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	9.41	ChemAxon
pKa (Strongest Basic)	4.36	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	177.17 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	71.48 m³·mol⁻¹	ChemAxon
Polarizability	25.92 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

SMPDB Pathways:

Flavin biosynthesis

PW001971

KEGG Pathways:

Methane metabolism ec00680
Microbial metabolism in diverse environments ec01120
Riboflavin metabolism ec00740

EcoCyc Pathways:

Not Available

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0903-9440000000-d4b6a6cff43cc761315f	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-056r-6294350000-61d4d076b5309ed14bcb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-056r-1190000000-2514b630f375b2189bfe	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-08fu-9750000000-779ce19c1a0e6b0c6932	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9300000000-2f9fc8d8f57a4b3ca8c6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01x0-5490000000-40e672b419cf2a89e723	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9210000000-e4e8a4b406ad4dfd459f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9200000000-0e769fc743b8cee3b542	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View 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
WACKER H, HARVEY RA, WINESTOCK CH, PLAUT GW: 4-(1'-D-RIBITYLAMINO)-5-AMINO-2,6-DIHYDROXYPYRIMIDINE, THE SECOND PRODUCT OF THE RIBOFLAVIN SYNTHETASE REACTION. J Biol Chem. 1964 Oct;239:3493-7. Pubmed: 14245407

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	15934
HMDB ID	HMDB11106
Pubchem Compound ID	221
Kegg ID	C04732
ChemSpider ID	216
Wikipedia ID	Not Available
BioCyc ID	Not 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.

Protein Details

3. Phosphatase ybjI

General function:: Involved in catalytic activity
Specific function:: Catalyzes the dephosphorylation of the artificial chromogenic substrate p-nitrophenyl phosphate (pNPP) and of the natural substrates FMN and beta-glucose 1-phosphate
Gene Name:: ybjI
Uniprot ID:: P75809
Molecular weight:: 30196

Protein Details

4. 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB

General function:: riboflavin biosynthetic process
Specific function:: Catalyzes the dephosphorylation of 5-amino-6-(5-phospho-D-ribitylamino)uracil, and thus could be involved in the riboflavin biosynthesis pathway (PubMed:24123841). Is also able to dephosphorylate flavin mononucleotide (FMN) and other phosphoric acid esters (PubMed:16990279) (PubMed:24123841). YigB is important for the formation of dormant persister cells (PubMed:18519731).
Gene Name:: yigB
Uniprot ID:: P0ADP0
Molecular weight:: 27121

Reactions

5-amino-6-(5-phospho-D-ribitylamino)uracil + H(2)O = 5-amino-6-(D-ribitylamino)uracil + phosphate

5-Amino-6-ribitylamino uracil (ECMDB04145) (M2MDB000635)

Structure for #<Compound:0xa27bb234>

Enzymes

Reactions

Reactions

Reactions