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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-22 00:39:03 UTC
Update Date2021-10-01 16:54:51 UTC
HMDB IDHMDB0301520
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-hydroxynona-5,7-dienoyl-CoA
Description3-hydroxynona-5,7-dienoyl-coa is an acyl-CoA or acyl-coenzyme A. More specifically, it is a 3-hydroxynona-5_7-dienoic acid thioester of coenzyme A. 3-hydroxynona-5,7-dienoyl-coa is an acyl-CoA with 9 fatty acid group as the acyl moiety attached to coenzyme A. Coenzyme A was discovered in 1946 by Fritz Lipmann (Journal of Biological Chemistry (1946) 162 (3): 743–744) and its structure was determined in the early 1950s at the Lister Institute in London. Coenzyme A is a complex, thiol-containing molecule that is naturally synthesized from pantothenate (vitamin B5), which is found in various foods such as meat, vegetables, cereal grains, legumes, eggs, and milk. More specifically, coenzyme A (CoASH or CoA) consists of a beta-mercaptoethylamine group linked to the vitamin pantothenic acid (B5) through an amide linkage and 3'-phosphorylated ADP. Coenzyme A is synthesized in a five-step process that requires four molecules of ATP, pantothenate and cysteine. It is believed that there are more than 1100 types of acyl-CoA’s in the human body, which also corresponds to the number of acylcarnitines in the human body. Acyl-CoAs exists in all living species, ranging from bacteria to plants to humans. The general role of acyl-CoA’s is to assist in transferring fatty acids from the cytoplasm to mitochondria. This process facilitates the production of fatty acids in cells, which are essential in cell membrane structure. Acyl-CoA's are also susceptible to beta oxidation, forming, ultimately, acetyl-CoA. Acetyl-CoA can enter the citric acid cycle, eventually forming several equivalents of ATP. In this way, fats are converted to ATP -- or biochemical energy. Acyl-CoAs can be classified into 9 different categories depending on the size of their acyl-group: 1) short-chain acyl-CoAs; 2) medium-chain acyl-CoAs; 3) long-chain acyl-CoAs; and 4) very long-chain acyl-CoAs; 5) hydroxy acyl-CoAs; 6) branched chain acyl-CoAs; 7) unsaturated acyl-CoAs; 8) dicarboxylic acyl-CoAs and 9) miscellaneous acyl-CoAs. Short-chain acyl-CoAs have acyl-groups with two to four carbons (C2-C4), medium-chain acyl-CoAs have acyl-groups with five to eleven carbons (C5-C11), long-chain acyl-CoAs have acyl-groups with twelve to twenty carbons (C12-C20) while very long-chain acyl-CoAs have acyl groups with more than 20 carbons. 3-hydroxynona-5,7-dienoyl-coa is therefore classified as a medium chain acyl-CoA. The oxidative degradation of fatty acids is a two-step process, catalyzed by acyl-CoA synthetase/synthase. Fatty acids are first converted to their acyl phosphate, the precursor to acyl-CoA. The latter conversion is mediated by acyl-CoA synthase. Three types of acyl-CoA synthases are employed, depending on the chain length of the fatty acid. 3-hydroxynona-5,7-dienoyl-coa, being a medium chain acyl-CoA is a substrate for medium chain acyl-CoA synthase. The second step of fatty acid degradation is beta oxidation. Beta oxidation occurs in mitochondria and, in the case of very long chain acyl-CoAs, the peroxisome. After its formation in the cytosol, 3-hydroxynona-5,7-dienoyl-CoA is transported into the mitochondria, the locus of beta oxidation. Transport of 3-hydroxynona-5,7-dienoyl-CoA into the mitochondria requires carnitine palmitoyltransferase 1 (CPT1), which converts 3-hydroxynona-5,7-dienoyl-CoA into 3-hydroxynona-5_7-dienoylcarnitine, which gets transported into the mitochondrial matrix. Once in the matrix, 3-hydroxynona-5_7-dienoylcarnitine is converted back to 3-hydroxynona-5,7-dienoyl-CoA by CPT2, whereupon beta-oxidation can begin. Beta oxidation of 3-hydroxynona-5,7-dienoyl-CoA occurs in four steps. First, since 3-hydroxynona-5,7-dienoyl-CoA is a medium chain acyl-CoA it is the substrate for a medium chain acyl-CoA dehydrogenase, which catalyzes dehydrogenation of 3-hydroxynona-5,7-dienoyl-CoA, creating a double bond between the alpha and beta carbons. FAD is the hydrogen acceptor, yielding FADH2. Second, Enoyl-CoA hydrase catalyzes the addition of water across the newly formed double bond to make an alcohol. Third, 3-hydroxyacyl-CoA dehydrogenase oxidizes the alcohol group to a ketone and NADH is produced from NAD+. Finally, Thiolase cleaves between the alpha carbon and ketone to release one molecule of acetyl-CoA and a new acyl-CoA which is now 2 carbons shorter. This four-step process repeats until 3-hydroxynona-5,7-dienoyl-CoA has had all its carbons removed from the chain, leaving only acetyl-CoA. Beta oxidation, as well as alpha-oxidation, also occurs in the peroxisome. The peroxisome handles beta oxidation of fatty acids that have more than 20 carbons in their chain because the peroxisome contains very-long-chain Acyl-CoA synthetases and dehydrogenases. The heart primarily metabolizes fat for energy and Acyl-CoA metabolism has been identified as a critical molecule in early-stage heart muscle pump failure. Cellular acyl-CoA content also correlates with insulin resistance, suggesting that it can mediate lipotoxicity in non-adipose tissues. Acyl-CoA: diacylglycerol acyltransferase (DGAT) plays an important role in energy metabolism on account of key enzyme in triglyceride biosynthesis. The study of acyl-CoAs is an active area of research and it is likely that many novel acyl-CoAs will be discovered in the coming years. It is also likely that many novel roles in health and disease will be uncovered for these molecules.
Structure
Thumb
Synonyms
ValueSource
4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-N-[2-({2-[(3-hydroxynona-5,7-dienoyl)sulfanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-3,3-dimethylbutanimidateGenerator
4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-N-[2-({2-[(3-hydroxynona-5,7-dienoyl)sulphanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-3,3-dimethylbutanimidateGenerator
4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-N-[2-({2-[(3-hydroxynona-5,7-dienoyl)sulphanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-3,3-dimethylbutanimidic acidGenerator
Chemical FormulaC30H48N7O18P3S
Average Molecular Weight919.73
Monoisotopic Molecular Weight919.198939902
IUPAC Name{[5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-({[hydroxy({[hydroxy(3-hydroxy-3-{[2-({2-[(3-hydroxynona-5,7-dienoyl)sulfanyl]ethyl}carbamoyl)ethyl]carbamoyl}-2,2-dimethylpropoxy)phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-3-yl]oxy}phosphonic acid
Traditional Name[5-(6-aminopurin-9-yl)-4-hydroxy-2-({[hydroxy([hydroxy(3-hydroxy-3-{[2-({2-[(3-hydroxynona-5,7-dienoyl)sulfanyl]ethyl}carbamoyl)ethyl]carbamoyl}-2,2-dimethylpropoxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-3-yl]oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
CC=CC=CCC(O)CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N
InChI Identifier
InChI=1S/C30H48N7O18P3S/c1-4-5-6-7-8-18(38)13-21(40)59-12-11-32-20(39)9-10-33-28(43)25(42)30(2,3)15-52-58(49,50)55-57(47,48)51-14-19-24(54-56(44,45)46)23(41)29(53-19)37-17-36-22-26(31)34-16-35-27(22)37/h4-7,16-19,23-25,29,38,41-42H,8-15H2,1-3H3,(H,32,39)(H,33,43)(H,47,48)(H,49,50)(H2,31,34,35)(H2,44,45,46)
InChI KeyQUYSJENPZFIDRT-UHFFFAOYSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effectNot Available
DispositionNot Available
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP0.26ALOGPS
logP-4.5ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.01ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area383.86 ŲChemAxon
Rotatable Bond Count25ChemAxon
Refractivity208.19 m³·mol⁻¹ChemAxon
Polarizability85.87 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+272.94332859911
AllCCS[M+H-H2O]+273.48132859911
AllCCS[M+Na]+272.23132859911
AllCCS[M+NH4]+272.39732859911
AllCCS[M-H]-273.39532859911
AllCCS[M+Na-2H]-278.58432859911
AllCCS[M+HCOO]-284.28632859911
DeepCCS[M+H]+244.67530932474
DeepCCS[M-H]-242.7830932474
DeepCCS[M-2H]-276.01630932474
DeepCCS[M+Na]+251.07430932474

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
MSMass Spectrum (Electron Ionization)Not Available2022-08-06Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-5,7-dienoyl-CoA 10V, Positive-QTOFsplash10-0uk9-1100000139-bbdc156f3a86115640d42021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-5,7-dienoyl-CoA 20V, Positive-QTOFsplash10-01p9-1400000291-e55efaba5e6d2ddd60262021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-5,7-dienoyl-CoA 40V, Positive-QTOFsplash10-03di-1001900000-23c40d12e3dccbd574332021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-5,7-dienoyl-CoA 10V, Negative-QTOFsplash10-014i-0000000009-1061005c14c5ab6917462021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-5,7-dienoyl-CoA 20V, Negative-QTOFsplash10-0lmi-7400201398-bc6987fa6f89e823708a2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-hydroxynona-5,7-dienoyl-CoA 40V, Negative-QTOFsplash10-0py1-5502611933-b4a5290c11327ea25b9a2021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Abe T, Fujino T, Fukuyama R, Minoshima S, Shimizu N, Toh H, Suzuki H, Yamamoto T: Human long-chain acyl-CoA synthetase: structure and chromosomal location. J Biochem. 1992 Jan;111(1):123-8. [PubMed:1607358 ]
  2. Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]