1-(5-phosphoribosyl)-5'-AMP (YMDB00868)

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Identification

YMDB ID

YMDB00868

Name

1-(5-phosphoribosyl)-5'-AMP

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Phosphoribosyl-AMP, also known as 5-phosphoribosyl-AMP, belongs to the class of organic compounds known as purine ribonucleoside monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached. In yeast, phosphoribosyl-AMP is involved in the metabolic pathway called the histidine biosynthesis pathway. Based on a literature review very few articles have been published on Phosphoribosyl-AMP.

Structure

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

Synonyms

1-(5-Phosphoribosyl)-AMP
5-phosphoribosyl-AMP
N1-(5-Phospho-D-ribosyl)-AMP
Phosphoribosyl-AMP
1-(5-Phospho-beta-D-ribosyl)-AMP
1-(5-Phospho-b-D-ribosyl)-AMP
1-(5-Phospho-β-D-ribosyl)-AMP

CAS number

Not Available

Weight

Average: 559.3157
Monoisotopic: 559.071673493

InChI Key

RTQMRTSPTLIIHM-KEOHHSTQSA-N

InChI

InChI=1S/C15H23N5O14P2/c16-12-7-13(18-4-19(12)14-10(23)8(21)5(33-14)1-31-35(25,26)27)20(3-17-7)15-11(24)9(22)6(34-15)2-32-36(28,29)30/h3-6,8-11,14-16,21-24H,1-2H2,(H2,25,26,27)(H2,28,29,30)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1

IUPAC Name

{[(2R,3S,4R,5R)-5-{1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-6-imino-6,9-dihydro-1H-purin-9-yl}-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional IUPAC Name

Phosphoribosyl-AMP

Chemical Formula

C₁₅H₂₃N₅O₁₄P₂

SMILES

O[C@@H]1[C@@H](COP(O)(O)=O)O[C@H]([C@@H]1O)N1C=NC2=C1N=CN([C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O)C2=N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as purine ribonucleoside monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside monophosphates

Alternative Parents

Substituents

Purine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Imidazopyrimidine
Purine
Monoalkyl phosphate
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Imidolactam
Heteroaromatic compound
Imidazole
Tetrahydrofuran
Azole
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Azacycle
Organopnictogen compound
Alcohol
Organic oxide
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

AMP-sugar (CHEBI:18374 )

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	6.38 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-4.2	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	0.65	ChemAxon
pKa (Strongest Basic)	5.95	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	290.17 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	122.54 m³·mol⁻¹	ChemAxon
Polarizability	45.4 Å³	ChemAxon
Number of Rings	4	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

Not Available

Organoleptic Properties

Not Available

SMPDB Pathways

Histidine Biosynthesis

PW002418

KEGG Pathways

Histidine metabolism

ec00340

SMPDB Reactions

Phosphoribosyl pyrophosphate + Adenosine triphosphate + hydron → Pyrophosphate + 1-(5-phosphoribosyl)-5'-AMP

KEGG Reactions

1-(5-phosphoribosyl)-5'-AMP + water → 1-(5-phospho-D-ribosyl)-5-[(5-phospho-D-ribosylamino)methylideneamino]imidazole-4-carboxamide

water + 5-phosphoribosyl-ATP → Pyrophosphate + 1-(5-phosphoribosyl)-5'-AMP + hydron

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 (1 TMS) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("Phosphoribosyl-AMP,1TMS,#1" TMS) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_16) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_17) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000t-0429120000-498a95153bece6824f93	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-001i-0925000000-814fabe53ab8f719f35f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001j-0944000000-4ff1b000ce081e879bbf	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-05bb-6409070000-14dd7aebd9e4f041a818	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004j-9304000000-c370f862b64f5520c773	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-b35331ba878a60224a03	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03dj-0068890000-8f61f6ddf1c5bd103778	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-0093100000-4dee179798c1c63b8122	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0k9t-9467000000-f51db55115fa158f973b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-1000090000-97733644c5f3e9484c42	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9001000000-72d8b1d9bc96034853b7	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
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

References

References:

Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
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
Keesey, J. K. Jr, Bigelis, R., Fink, G. R. (1979). "The product of the his4 gene cluster in Saccharomyces cerevisiae. A trifunctional polypeptide." J Biol Chem 254:7427-7433.379004

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	18374
HMDB ID	HMDB0012276
Pubchem Compound ID	11988267
Kegg ID	C02741
ChemSpider ID	24808237
FOODB ID	FDB028908
Wikipedia ID	Not Available
BioCyc ID	Not Available

Enzymes

Protein Details

1. ATP phosphoribosyltransferase

General function:: Involved in ATP phosphoribosyltransferase activity
Specific function:: Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of the enzymatic activity
Gene Name:: HIS1
Uniprot ID:: P00498
Molecular weight:: 32266.09961

Reactions

1-(5-phospho-D-ribosyl)-ATP + diphosphate → ATP + 5-phospho-alpha-D-ribose 1-diphosphate.

Protein Details

2. Histidine biosynthesis trifunctional protein

General function:: Involved in oxidoreductase activity
Specific function:: 1-(5-phosphoribosyl)-AMP + H(2)O = 1-(5- phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4-carboxamide
Gene Name:: HIS4
Uniprot ID:: P00815
Molecular weight:: 87720.5

Reactions

1-(5-phosphoribosyl)-AMP + H(2)O → 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide.
1-(5-phosphoribosyl)-ATP + H(2)O → 1-(5-phosphoribosyl)-AMP + diphosphate.
L-histidinol + H(2)O + 2 NAD(+) → L-histidine + 2 NADH.

Structure for #<Compound:0xac34a1dc>

Enzymes

Reactions

Reactions