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1,4-Dihydroxy-2-naphthoyl-CoA (M2MDB000881)

Record Information
Version2.0
Creation Date2012-05-31 14:23:53 -0600
Update Date2015-09-17 15:41:52 -0600
Secondary Accession Numbers
  • ECMDB20032
Identification
Name:1,4-Dihydroxy-2-naphthoyl-CoA
Description1,4-dihydroxy-2-naphthoyl-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. 1,4-Dihydroxy-2-naphthoyl-CoA is involved menaquinone biosynthetic pathway. 1,4-dihydroxy-2-naphthoate (DHNA) is a branch point metabolite leading to the biosynthesis of menaquinone (vitamin K2 in bacteria) and begins with the conjugation of DHNA with the CoA moiety via 1,4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase. (PMID 20643650)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 1,4-Dihydroxy-2-naphthoate-CoA
  • 1,4-Dihydroxy-2-naphthoic acid-CoA
  • DHNA-CoA
Chemical Formula:C32H38N7O19P3S
Weight:Average: 949.67
Monoisotopic: 949.117798519
InChI Key:PYTINLGPKDJURZ-HSJNEKGZSA-J
InChI:InChI=1S/C32H42N7O19P3S/c1-32(2,26(44)29(45)35-8-7-21(41)34-9-10-62-31(46)18-11-19(40)16-5-3-4-6-17(16)23(18)42)13-55-61(52,53)58-60(50,51)54-12-20-25(57-59(47,48)49)24(43)30(56-20)39-15-38-22-27(33)36-14-37-28(22)39/h3-6,11,14-15,20,24-26,30,40,42-44H,7-10,12-13H2,1-2H3,(H,34,41)(H,35,45)(H,50,51)(H,52,53)(H2,33,36,37)(H2,47,48,49)/p-4/t20-,24-,25-,26+,30-/m1/s1
CAS number:Not Available
IUPAC Name:(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)-N-(2-{[2-(1,4-dihydroxynaphthalene-2-carbonylsulfanyl)ethyl]-C-hydroxycarbonimidoyl}ethyl)-2-hydroxy-3,3-dimethylbutanimidic acid
Traditional IUPAC Name:(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]-N-(2-{[2-(1,4-dihydroxynaphthalene-2-carbonylsulfanyl)ethyl]-C-hydroxycarbonimidoyl}ethyl)-2-hydroxy-3,3-dimethylbutanimidic acid
SMILES:[H][C@](O)(C([O-])=NCCC([O-])=NCCSC(=O)C1=C([O-])C2=CC=CC=C2C([O-])=C1)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 acyl coas. These are organic compounds containing a coenzyme A substructure linked to an acyl chain.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acyl thioesters
Direct ParentAcyl 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
  • 2-naphthalenecarboxylic acid or derivatives
  • Beta amino acid or derivatives
  • Glycosyl compound
  • N-glycosyl compound
  • 1-naphthol
  • Salicylic acid or derivatives
  • 6-aminopurine
  • Pentose monosaccharide
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Naphthalene
  • Thiobenzoic acid or derivatives
  • Imidazopyrimidine
  • Purine
  • Hydroquinone
  • Monoalkyl phosphate
  • 1-hydroxy-2-unsubstituted benzenoid
  • Aminopyrimidine
  • Fatty amide
  • Monosaccharide
  • N-acyl-amine
  • N-substituted imidazole
  • Imidolactam
  • Organic phosphoric acid derivative
  • Benzenoid
  • Alkyl phosphate
  • Phosphoric acid ester
  • Pyrimidine
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Vinylogous acid
  • Carboxamide group
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Thiocarboxylic acid ester
  • Amino acid or derivatives
  • Carbothioic s-ester
  • Organoheterocyclic compound
  • Azacycle
  • Thiocarboxylic acid or derivatives
  • Oxacycle
  • Sulfenyl compound
  • Carboxylic acid derivative
  • Primary amine
  • Organic nitrogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organooxygen compound
  • Organosulfur compound
  • Carbonyl group
  • Alcohol
  • Amine
  • Organonitrogen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-4
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility5.63 g/LALOGPS
logP0.55ALOGPS
logP-1.2ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.79ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count21ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area411.07 ŲChemAxon
Rotatable Bond Count21ChemAxon
Refractivity214.33 m³·mol⁻¹ChemAxon
Polarizability86.05 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
1,4-Dihydroxy-2-naphthoyl-CoA + Water > Coenzyme A + 1,4-Dihydroxy-2-naphthoic acid + Hydrogen ion
Hydrogen ion + 2-Succinylbenzoyl-CoA > 1,4-Dihydroxy-2-naphthoyl-CoA + Water
2-Succinylbenzoyl-CoA <> 1,4-Dihydroxy-2-naphthoyl-CoA + Water
4-(2-Carboxyphenyl)-4-oxobutanoyl-CoA > 1,4-Dihydroxy-2-naphthoyl-CoA + Water
2-Succinylbenzoyl-CoA + Hydrogen ion > Water + 1,4-dihydroxy-2-naphthoyl-CoA + 1,4-Dihydroxy-2-naphthoyl-CoA
1,4-dihydroxy-2-naphthoyl-CoA + Water + 1,4-Dihydroxy-2-naphthoyl-CoA > Coenzyme A + Hydrogen ion + 1,4-dihydroxy-2-naphthoate
1,4-dihydroxy-2-naphthoate + Hydrogen ion + Farnesylfarnesylgeranyl-PP + 1,4-Dihydroxy-2-naphthoyl-CoA > Carbon dioxide + Pyrophosphate + 2-Demethylmenaquinol 8
Octaprenyl diphosphate + 1,4-dihydroxy-2-naphthoate + Hydrogen ion + Octaprenyl diphosphate + 1,4-Dihydroxy-2-naphthoyl-CoA > Carbon dioxide + Pyrophosphate + 2-Demethylmenaquinol 8
SMPDB Pathways:
Menaquinol biosythesisPW001897 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Metabolic pathways eco01100
  • Ubiquinone and other terpenoid-quinone biosynthesis ec00130
EcoCyc Pathways:
  • 1,4-dihydroxy-2-naphthoate biosynthesis I PWY-5837
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-1955100102-0fde5542c1568ba82d5fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01p9-0952200000-b4a4ffa5cb62c6d358b5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01p9-2932000000-e29227c090d087e2f7dbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0569-2911021403-1862354be630ac81b2f8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-2900100001-ce85346d9f708fe780a1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-057i-5900000000-27976ab9b9be4acd3a34View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0000000009-aa47b7bee7fae576c874View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f79-0422712419-78e152c0761b599e872cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-0201900000-e76cf5fd5292c30e7132View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0000000009-b768a8f4d0fc97388be0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufr-4831204509-021f2308985916c473c7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0f92-7102614902-c2caf4b4e82fedd2e2c0View in MoNA
References
References:
  • Jiang, M., Chen, M., Guo, Z. F., Guo, Z. (2010). "A bicarbonate cofactor modulates 1,4-dihydroxy-2-naphthoyl-coenzyme a synthase in menaquinone biosynthesis of Escherichia coli." J Biol Chem 285:30159-30169. Pubmed: 20643650
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID52668
HMDB IDHMDB0304010
Pubchem Compound ID11954202
Kegg IDC15547
ChemSpider ID10128497
Wikipedia IDNot Available
BioCyc IDCPD-9925
EcoCyc IDCPD-9925

Enzymes

Protein Details
1. Naphthoate synthase
General function:
Involved in catalytic activity
Specific function:
Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4- dihydroxy-2-naphthoyl-CoA (DHNA-CoA)
Gene Name:
menB
Uniprot ID:
P0ABU0
Molecular weight:
31633
Reactions
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H(2)O.
Protein Details
2. 1,4-dihydroxy-2-naphthoate octaprenyltransferase
General function:
Involved in transferase activity
Specific function:
Conversion of 1,4-dihydroxy-2-naphthoate (DHNA) to dimethylmenaquinone (DMK). Attaches octaprenylpyrophosphate, a membrane-bound 40-carbon side chain to DHNA. The conversion of DHNA to DMK proceeds in three stages:the removal of the carboxyl group of DHNA as CO(2), the attachment of the isoprenoid side chain, and a quinol-to-quinone oxidation, which is thought to be spontaneous
Gene Name:
menA
Uniprot ID:
P32166
Molecular weight:
33594
Reactions
An all-trans-polyprenyl diphosphate + 1,4-dihydroxy-2-naphthoate = a demethylmenaquinol + diphosphate + CO(2).
Protein Details
3. Acyl-CoA thioester hydrolase YbgC
General function:
Involved in hydrolase activity
Specific function:
Thioesterase that appears to be involved in phospholipid metabolism. Some specific acyl-ACPs could be physiological substrates. Displays acyl-CoA thioesterase activity on malonyl-CoA in vitro, catalyzing the hydrolysis of the thioester bond
Gene Name:
ybgC
Uniprot ID:
P0A8Z3
Molecular weight:
15562