ECMDB: 3-Oxo-5,6-dehydrosuberyl-CoA (ECMDB21172) (M2MDB001581)

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

Proteins (200)

Record Information

Version

2.0

Creation Date

2012-07-30 14:54:45 -0600

Update Date

2015-06-03 17:20:48 -0600

Secondary Accession Numbers

ECMDB21172

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

Synonyms:

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

Chemical Formula:

C₂₉H₄₄N₇O₂₀P₃S

Weight:

Average: 935.681
Monoisotopic: 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

Description

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 bisphosphate
Purine ribonucleoside 3',5'-bisphosphate
Ribonucleoside 3'-phosphate
Pentose-5-phosphate
Pentose phosphate
Beta amino acid or derivatives
Glycosyl compound
N-glycosyl compound
6-aminopurine
Pentose monosaccharide
Organic pyrophosphate
Monosaccharide phosphate
Purine
Imidazopyrimidine
Medium-chain fatty acid
Aminopyrimidine
Hydroxy fatty acid
Monoalkyl phosphate
1,3-dicarbonyl compound
Unsaturated fatty acid
Fatty amide
Monosaccharide
N-acyl-amine
N-substituted imidazole
Organic phosphoric acid derivative
Fatty acid
Phosphoric acid ester
Imidolactam
Alkyl phosphate
Pyrimidine
Tetrahydrofuran
Imidazole
Azole
Heteroaromatic compound
Carboxamide group
Thiocarboxylic acid ester
Amino acid
Carbothioic s-ester
Secondary carboxylic acid amide
Secondary alcohol
Ketone
Amino acid or derivatives
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Oxacycle
Thiocarboxylic acid or derivatives
Azacycle
Organoheterocyclic compound
Sulfenyl compound
Organic oxygen compound
Organopnictogen compound
Carbonyl group
Primary amine
Organic oxide
Alcohol
Amine
Hydrocarbon derivative
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organosulfur compound
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 g/L	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:

SMPDB Pathways:

Phenylalanine metabolism	PW000921
Phenylethylamine metabolism	PW002027

KEGG Pathways:

Benzoate degradation via hydroxylation ec00362
Phenylalanine metabolism ec00360

EcoCyc Pathways:

phenylacetate degradation I (aerobic) PWY0-321

Concentrations

Not Available

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
MS	Mass Spectrum (Electron Ionization)	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
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

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	Not Available
Wikipedia ID	Not Available
BioCyc ID	CPD0-2364
EcoCyc ID	CPD0-2364

Enzymes

Protein Details

1. Beta-ketoadipyl-CoA thiolase

General function:: Involved in transferase activity, transferring acyl groups other than amino-acyl groups
Specific function:: Catalyzes thiolytic cleavage of beta-ketoadipyl-CoA to succinyl-CoA and acetyl-CoA
Gene Name:: paaJ
Uniprot ID:: P0C7L2
Molecular weight:: 42276

Reactions

Succinyl-CoA + acetyl-CoA = CoA + 3-oxoadipyl-CoA.
2,3-dehydroadipyl-CoA + acetyl-CoA = CoA + 3-oxo-5,6-dehydrosuberyl-CoA.

Protein Details

2. Probable enoyl-CoA hydratase paaG

General function:: Involved in catalytic activity
Specific function:: Could possibly oxidize fatty acids using specific components
Gene Name:: paaG
Uniprot ID:: P77467
Molecular weight:: 28404

Reactions

2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-oxepin-2(3H)-ylideneacetyl-CoA.

Protein Details

3. Protein maoC

General function:: Involved in oxidoreductase activity
Specific function:: Specific function unknown
Gene Name:: maoC
Uniprot ID:: P77455
Molecular weight:: 73002

Reactions

2-oxepin-2(3H)-ylideneacetyl-CoA + H(2)O = 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde.
3-oxo-5,6-dehydrosuberyl-CoA semialdehyde + NADP(+) + H(2)O = 3-oxo-5,6-dehydrosuberyl-CoA + NADPH.

3-Oxo-5,6-dehydrosuberyl-CoA (ECMDB21172) (M2MDB001581)

Structure for #<Compound:0xa63a671c>

Enzymes

Reactions

Reactions

Reactions