ECMDB: Lipoyl-AMP (ECMDB20170) (M2MDB001017)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (1)XML

Proteins (239)

Record Information

Version

2.0

Creation Date

2012-05-31 14:31:13 -0600

Update Date

2015-06-03 17:19:27 -0600

Secondary Accession Numbers

ECMDB20170

Identification

Name:

Lipoyl-AMP

Description

Lipoyl-amp belongs to the class of Purine Ribonucleoside Monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached. (inferred from compound structure)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-ylmethoxy-hydroxyphosphoryl 5-(dithiolan-3-yl)pentanoate
(2R,3S,4R,5R)-5-(6-Aminopurin-9-yl)-3,4-dihydroxyoxolan-2-ylmethoxy-hydroxyphosphoryl 5-(dithiolan-3-yl)pentanoic acid
5'-O-{5-(1,2-Dithiolan-3-yl)pentanoyloxy}(hydroxy)phosphoryladenosine
Lipoyl-AMP

Chemical Formula:

C₁₈H₂₆N₅O₈PS₂

Weight:

Average: 535.532
Monoisotopic: 535.096040725

InChI Key:

QWEGOCJRZOKSOE-NLJBGGCZSA-N

InChI:

InChI=1S/C18H26N5O8PS2/c19-16-13-17(21-8-20-16)23(9-22-13)18-15(26)14(25)11(30-18)7-29-32(27,28)31-12(24)4-2-1-3-10-5-6-33-34-10/h8-11,14-15,18,25-26H,1-7H2,(H,27,28)(H2,19,20,21)/t10?,11-,14-,15-,18-/m1/s1

CAS number:

Not Available

IUPAC Name:

{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[5-(1,2-dithiolan-3-yl)pentanoyl]oxy})phosphinic acid

Traditional IUPAC Name:

Lipoyl-AMP

SMILES:

NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(=O)OC(=O)CCCCC2CCSS2)[C@@H](O)[C@H]1O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as 5'-acylphosphoadenosines. These are ribonucleoside derivatives containing an adenoside moiety, where the phosphate group is acylated.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

5'-acylphosphoadenosines

Alternative Parents

Substituents

5'-acylphosphoadenosine
Pentose-5-phosphate
Pentose phosphate
Lipoic_acid_derivative
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
6-aminopurine
Pentose monosaccharide
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
Acyl phosphate
Monosaccharide
Imidolactam
N-substituted imidazole
Alkyl phosphate
Organic phosphoric acid derivative
Pyrimidine
Phosphoric acid ester
Azole
Dithiolane
Imidazole
Heteroaromatic compound
1,2-dithiolane
Tetrahydrofuran
Organic disulfide
Secondary alcohol
Amino acid or derivatives
1,2-diol
Carboxylic acid salt
Organoheterocyclic compound
Azacycle
Monocarboxylic acid or derivatives
Oxacycle
Carboxylic acid derivative
Primary amine
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organic oxygen compound
Organopnictogen compound
Amine
Organonitrogen compound
Organooxygen compound
Alcohol
Organic salt
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dithiolanes (CHEBI:55451 )
purine ribonucleoside 5'-monophosphate (CHEBI:55451 )
acyclic mixed acid anhydride (CHEBI:55451 )

Physical Properties

State:

Not Available

Charge:

-1

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	1.12 g/L	ALOGPS
logP	0.25	ALOGPS
logP	-2.3	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	0.83	ChemAxon
pKa (Strongest Basic)	4.99	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	192.14 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	124.95 m³·mol⁻¹	ChemAxon
Polarizability	50.71 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:

Cytoplasm

Reactions:

Adenosine triphosphate + Lipoic acid > Lipoyl-AMP + Pyrophosphate
Lipoyl-AMP > Adenosine monophosphate + lipoate (protein bound)
Adenosine triphosphate + Lipoic acid <> Pyrophosphate + Lipoyl-AMP
Lipoyl-AMP + Apoprotein <> Protein N6-(lipoyl)lysine + Adenosine monophosphate
Hydrogen ion + Lipoic acid + Adenosine triphosphate > Lipoyl-AMP + Pyrophosphate
Adenosine triphosphate + lipoate > Pyrophosphate + Lipoyl-AMP
Lipoyl-AMP + protein > protein N(6)-(lipoyl)lysine + Adenosine monophosphate
Adenosine triphosphate + lipoate + Lipoyl-AMP + Apoprotein <> Pyrophosphate + Protein N6-(lipoyl)lysine + Adenosine monophosphate
lipoate + Adenosine triphosphate > Lipoyl-AMP + Pyrophosphate + Lipoyl-AMP
Lipoyl-AMP + apoprotein + Lipoyl-AMP > Protein N6-(lipoyl)lysine + Adenosine monophosphate
(R)-lipoic acid + Adenosine triphosphate + Hydrogen ion + Lipoic acid > Pyrophosphate + Lipoyl-AMP + Lipoyl-AMP
Lipoyl-AMP + a [lipoyl-carrier protein]-L-lysine + Lipoyl-AMP > Adenosine monophosphate + Hydrogen ion + Protein N6-(lipoyl)lysine

SMPDB Pathways:

Lipoic acid metabolism

PW000770

KEGG Pathways:

Lipoic acid metabolism ec00785
Metabolic pathways eco01100

EcoCyc Pathways:

lipoate salvage I PWY0-522

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-02ds-3913010000-e06df70a38935bfec6ca	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-03xs-9852448000-ab8656a944a15acff0d2	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("Lipoyl-AMP,1TMS,#1" TMS) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0911020000-403226dda50e9b19c782	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-1900000000-09f2e5c022805e4e9fe4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-1900000000-8cffaab609f0ad97292d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-003r-3779560000-3583b9a6776d5e619ce6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-003r-5911000000-bd5c472188d51d73ad0c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003r-9500000000-b3956188225c40fb0715	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-0000090000-97f9a62a74dc17a227c7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0059-9100360000-0957a91a14ca65d00ed6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-01u0-9200000000-598cbfd3e15d0060e791	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0101090000-158a5093458bb19523bb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-55f0391000d477c8c77d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-0920000000-c5661a88a8e2cb7260af	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
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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	55451
HMDB ID	HMDB0059635
Pubchem Compound ID	23724672
Kegg ID	C16238
ChemSpider ID	26330628
Wikipedia ID	Not Available
BioCyc ID	LIPOYL-AMP
EcoCyc ID	LIPOYL-AMP

Enzymes

Protein Details

1. Lipoate-protein ligase A

General function:: Involved in catalytic activity
Specific function:: Catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of lipoate-dependent enzymes. Is also able to catalyze very poorly the transfer of lipoyl and octanoyl moiety from their acyl carrier protein
Gene Name:: lplA
Uniprot ID:: P32099
Molecular weight:: 37926

Reactions

ATP + lipoate = diphosphate + lipoyl-AMP.
Lipoyl-AMP + protein = protein N(6)-(lipoyl)lysine + AMP.

Lipoyl-AMP (ECMDB20170) (M2MDB001017)

Structure for #<Compound:0xb4562a70>

Enzymes

Reactions