ECMDB: 5-Amino-6-(5'-phosphoribitylamino)uracil (ECMDB21177) (M2MDB001586)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (3)XML

Proteins (381)

Record Information

Version

2.0

Creation Date

2012-07-30 14:54:47 -0600

Update Date

2015-09-17 15:41:18 -0600

Secondary Accession Numbers

ECMDB21177

Identification

Name:

5-Amino-6-(5'-phosphoribitylamino)uracil

Description

5-Amino-6-(5'-phosphoribitylamino)uracil is an intermediate in Riboflavin metabolism. 5-Amino-6-(5'-phosphoribitylamino)uracil is the; 3rd to last step in the synthesis of 7-Hydroxy-6-methyl-8-ribityl lumazine and is converted from 5-Amino-6-(5'-phosphoribosylamino)uracil via the enzyme 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193). It is then; converted to 4-(1-D-Ribitylamino)-5-amino-2,6-dihydroxypyrimidine via the enzyme Hydrolases (EC 3.1.3.- ).

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms:

1-(5-Amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-ylamino)-1-deoxy-5-O-phosphono-D-ribitol
1-(5-Amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-ylamino)-1-deoxy-D-ribitol 5-(dihydrogen phosphate)
1-(5-amino-2,6-dioxo-1,2,3,6-Tetrahydropyrimidin-4-ylamino)-1-deoxy-D-ribitol 5-(dihydrogen phosphoric acid)
1-[(5-Amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-1-deoxy-5-O-phosphono-D-ribitol
5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine
5-Amino-2,6-dioxy-4-(5'-phosphoribitylamino)pyrimidine
5-Amino-6-(5'-phospho-D-ribitylamino)uracil
5-Amino-6-(5'-phosphoribitylamino)uracil
5-Amino-6-(5-phospho-D-ribitylamino)uracil
5-Amino-6-(5-phosphoribitylamino)uracil
5-Amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate
5-amino-6-ribitylamino-2,4(1H,3H)-Pyrimidinedione 5'-phosphoric acid
5A6-5'PRbAU

Chemical Formula:

C₉H₁₇N₄O₉P

Weight:

Average: 356.2264
Monoisotopic: 356.073314674

InChI Key:

RQRINYISXYAZKL-UHFFFAOYSA-N

InChI:

InChI=1S/C9H17N4O9P/c10-5-7(12-9(18)13-8(5)17)11-1-3(14)6(16)4(15)2-22-23(19,20)21/h3-4,6,14-16H,1-2,10H2,(H2,19,20,21)(H3,11,12,13,17,18)

CAS number:

Not Available

IUPAC Name:

{[(2R,3S,4S)-5-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxy}phosphonic acid

Traditional IUPAC Name:

[(2R,3S,4S)-5-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxyphosphonic acid

SMILES:

NC1=C(NCC(O)C(O)C(O)COP(O)(O)=O)NC(=O)NC1=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Aminopyrimidine
Monoalkyl phosphate
Pyrimidone
Secondary aliphatic/aromatic amine
Hydropyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Lactam
Urea
Secondary alcohol
Organoheterocyclic compound
Polyol
Azacycle
Secondary amine
Primary amine
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Organopnictogen compound
Amine
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

ribitol phosphate (CHEBI:18247 )
aminouracil (CHEBI:18247 )
alditol 5-phosphate (CHEBI:18247 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	2.89 g/L	ALOGPS
logP	-2.5	ALOGPS
logP	-4.5	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	223.7 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	82.36 m³·mol⁻¹	ChemAxon
Polarizability	30.06 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	0	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:

Not Available

EcoCyc Pathways:

flavin biosynthesis I (bacteria and plants) RIBOSYN2-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-000j-7932000000-f99b2e65ef6ba20ea0f8	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0249000000-aad1afed0b055e36f1f2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-052f-2932000000-8ce6cdef86c0d6904216	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9810000000-0889d500d98fdc446282	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03mi-6926000000-99084eeb27c449bf8caf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004l-9100000000-7df2c276c4edd1cadab5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-c2c18ea089d342debbaf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0039000000-29673935259424dca664	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-052f-0490000000-f14bfba265a959aa7c3d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-6900000000-c2d4ad73928d0404741b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a6r-8009000000-122c5a4319e344f1a64b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-77766ee562ec0704b879	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004l-9100000000-4ea49ebd63ee36be8b96	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:

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

Links

External Links:

Resource	Link
CHEBI ID	18247
HMDB ID	HMDB03841
Pubchem Compound ID	333
Kegg ID	C04454
ChemSpider ID	18921533
Wikipedia ID	Not Available
BioCyc ID	CPD-1086
EcoCyc ID	CPD-1086

Enzymes

Protein Details

1. Riboflavin biosynthesis protein ribD

General function:: Involved in zinc ion binding
Specific function:: Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
Gene Name:: ribD
Uniprot ID:: P25539
Molecular weight:: 40338

Reactions

2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H(2)O = 5-amino-6-(5-phosphoribosylamino)uracil + NH(3).
5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH.

Protein Details

2. 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

3. 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-(5'-phosphoribitylamino)uracil (ECMDB21177) (M2MDB001586)

Structure for #<Compound:0x995bac2c>

Enzymes

Reactions

Reactions