5-Amino-6-(D-ribitylamino)uracil (YMDB00765)

Identification

YMDB ID

YMDB00765

Name

5-Amino-6-(D-ribitylamino)uracil

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

5-Amino-6-ribitylamino uracil, also known as 6-(1-D-ribitylamino)-5-aminouracil or 5-arpd, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 5-Amino-6-ribitylamino uracil is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-Amino-6-ribitylamino uracil exists in all living species, ranging from bacteria to humans. Within yeast, 5-amino-6-ribitylamino uracil participates in a number of enzymatic reactions. In particular, 1-deoxy-L-glycero-tetrulose 4-phosphate and 5-amino-6-ribitylamino uracil can be converted into 6,7-dimethyl-8-(D-ribityl)lumazine; which is mediated by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. In addition, riboflavin and 5-amino-6-ribitylamino uracil can be biosynthesized from 6,7-dimethyl-8-(D-ribityl)lumazine; which is mediated by the enzyme riboflavin synthase. In yeast, 5-amino-6-ribitylamino uracil is involved in the metabolic pathway called the riboflavin metabolism pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

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-(D-ribitylamino)uracil
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
5-a-RU
a-4-RAP
1-[(5-Amino-1,2,3,6-tetrahydro-2,6-dioxo-4-pyrimidinyl)amino]-1-deoxy-D-ribitol
4-(1'-D-Ribitylamino)-5-amino-2,6-dihydroxypyrimidine
4-(1’-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
4-(Ribitylamino)-5-aminouracil
4-Ribitylamino-5-amino-2,6-dihydroxypyrimidine
5-Amino-4-D-ribitylaminouracil
5-Amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
ARP
5-Amino-6-ribitylamino uracil

CAS number

Not Available

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

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

Chemical Formula

C₉H₁₆N₄O₆

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.

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

hydroxypyrimidine (CHEBI:15934 )
aminouracil (CHEBI:15934 )

Physical Properties

State

Not Available

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

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)	8.48	ChemAxon
pKa (Strongest Basic)	-2.7	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	25.82 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

Not Available

Organoleptic Properties

Not Available

SMPDB Pathways

Riboflavin metabolism

PW002443

KEGG Pathways

Methane metabolism	ec00680
Riboflavin metabolism	ec00740

SMPDB Reactions

Not Available

KEGG Reactions

Not Available

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0903-9440000000-d4b6a6cff43cc761315f	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_4_38) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("5-Amino-6-ribitylamino uracil,4TBDMS,#38" TMS) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-056r-1190000000-2514b630f375b2189bfe	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-08fu-9750000000-779ce19c1a0e6b0c6932	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9300000000-2f9fc8d8f57a4b3ca8c6	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01x0-5490000000-40e672b419cf2a89e723	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-9210000000-e4e8a4b406ad4dfd459f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9200000000-0e769fc743b8cee3b542	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0090000000-04a8c31cda1ce3aa2de8	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-054o-0490000000-f4be226ba3308c6193ea	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9700000000-b24f4f1baf9ef6a124b9	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-056r-0290000000-dbb8670827f983a8ba0f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-052g-2900000000-2170e047feac10873419	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9400000000-c7d08326dc254630e183	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer

References

References:

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

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	15934
HMDB ID	HMDB0011106
Pubchem Compound ID	14056325
Kegg ID	C04732
ChemSpider ID	167930
FOODB ID	FDB030561
Wikipedia ID	Not Available
BioCyc ID	Not Available

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.

5-Amino-6-(D-ribitylamino)uracil (YMDB00765)

Structure for #<Compound:0xad692398>

Enzymes

Reactions

Reactions