P. aeruginosa Metabolome Database: 3-Oxo-5,6-dehydrosuberyl-CoA (PAMDB001581)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB001581

Identification

Name:

3-Oxo-5,6-dehydrosuberyl-CoA

Description:

3-Oxo-5,6-dehydrosuberyl-CoA is a member of the chemical class known as Coenzyme A and Derivatives. These are derivative of vitamin B5 containing a 4'-phosphopantetheine moiety attached to a diphospho-adenosine.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

(5Z)-7-carboxy-3-oxohept-5-enoyl-CoA
(5Z)-7-carboxy-3-oxohept-5-enoyl-CoA

Chemical Formula:

C₂₉H₄₄N₇O₂₀P₃S

Average Molecular Weight:

935.681

Monoisotopic Molecular Weight:

935.157467109

InChI Key:

IFFFDKYRRUVOFP-NOQDIWQESA-N

InChI:

InChI=1S/C29H44N7O20P3S/c1-29(2,24(43)27(44)32-8-7-18(38)31-9-10-60-20(41)11-16(37)5-3-4-6-19(39)40)13-53-59(50,51)56-58(48,49)52-12-17-23(55-57(45,46)47)22(42)28(54-17)36-15-35-21-25(30)33-14-34-26(21)36/h3-4,14-15,17,22-24,28,42-43H,5-13H2,1-2H3,(H,31,38)(H,32,44)(H,39,40)(H,48,49)(H,50,51)(H2,30,33,34)(H2,45,46,47)/t17-,22-,23-,24+,28-/m1/s1

CAS number:

Not Available

IUPAC Name:

8-({2-[(3-{[(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)-6,8-dioxooct-3-enoic acid

Traditional IUPAC Name:

8-({2-[(3-{[(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)-6,8-dioxooct-3-enoic acid

SMILES:

[H][C@](O)(C(O)=NCCC(O)=NCCSC(=O)CC(=O)CC=CCC(O)=O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP(O)(O)=O

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as 3-oxo-acyl coas. These are organic compounds containing a 3-oxo acylated coenzyme A derivative.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl thioesters

Direct Parent

3-oxo-acyl CoAs

Alternative Parents

Substituents

Coenzyme a or derivatives
Purine ribonucleoside diphosphate
Purine ribonucleoside 3',5'-bisphosphate
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
6-aminopurine
Purine
Imidazopyrimidine
Medium-chain fatty acid
Monoalkyl phosphate
Aminopyrimidine
Fatty acid
Imidolactam
Alkyl phosphate
1,3-dicarbonyl compound
Unsaturated fatty acid
Pyrimidine
Primary aromatic amine
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
N-substituted imidazole
Monosaccharide
Saccharide
Heteroaromatic compound
Oxolane
Imidazole
Azole
Thiocarboxylic acid ester
Secondary alcohol
Ketone
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Sulfenyl compound
Thioether
Thiocarboxylic acid or derivatives
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Hydrocarbon derivative
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

acyl-CoA (CHEBI:63253 )

Physical Properties

State:

Not Available

Charge:

-4

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	5.46 mg/mL	ALOGPS
logP	0.05	ALOGPS
logP	-3.7	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	0.82	ChemAxon
pKa (Strongest Basic)	4.83	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	22	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	424.98 Å²	ChemAxon
Rotatable Bond Count	26	ChemAxon
Refractivity	204.36 m³·mol^-1	ChemAxon
Polarizability	83.17 Å³	ChemAxon
Number of Rings	3	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:

3-Oxo-5,6-dehydrosuberyl-CoA + Coenzyme A <> 5-Carboxy-2-pentenoyl-CoA + Acetyl-CoA
2-Oxepin-2(3H)-ylideneacetyl-CoA + 2 Water + NADP > 3-Oxo-5,6-dehydrosuberyl-CoA +2 Hydrogen ion + NADPH
3-Oxo-5,6-dehydrosuberyl-CoA semialdehyde + NADP + Water <> 3-Oxo-5,6-dehydrosuberyl-CoA + NADPH + Hydrogen ion
3-Oxo-5,6-dehydrosuberyl-CoA + Coenzyme A > 2,3-dehydroadipyl-CoA + Acetyl-CoA
3-Oxo-5,6-dehydrosuberyl-CoA semialdehyde + NADP + Water > 3-Oxo-5,6-dehydrosuberyl-CoA + NADPH

Pathways:

Benzoate degradation via hydroxylation pae00362
Phenylalanine metabolism pae00360

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kr-1964100305-916fd72811157d17a619	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000l-0952200000-f4eb0e1814a70fa1fd8c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-2931000000-bfb30f7e8ad78dce09cb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00lr-2911031315-3a6fab8577fcd8a04590	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-2910110001-797d85c7274c9134f1fb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-057i-6900000000-135442d87faa29036185	View in MoNA

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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	63253
HMDB ID	Not Available
Pubchem Compound ID	56927776
Kegg ID	C19945
ChemSpider ID	26333055
Wikipedia ID	Not Available
BioCyc ID	CPD0-2364
EcoCyc ID	CPD0-2364

3-Oxo-5,6-dehydrosuberyl-CoA (PAMDB001581)

Structure for 3-Oxo-5,6-dehydrosuberyl-CoA (PAMDB001581)