Molybdopterin cytosine dinucleotide (ECMDB21346) (M2MDB001744)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (1)
Record Information
Version2.0
Creation Date2012-07-30 14:55:23 -0600
Update Date2015-06-03 17:21:12 -0600
Secondary Accession Numbers
  • ECMDB21346
Identification
Name:Molybdopterin cytosine dinucleotide
DescriptionMolybdopterin cytosine dinucleotide is a member of the chemical class known as Pyrimidine Ribonucleoside Diphosphates. These are pyrimidine ribobucleotides with diphosphate group linked to the ribose moiety. MocA is a specific cytidylyltransferase involved in molybdopterin cytosine dinucleotide biosynthesis in Escherichia coli. (PMID 19542235) Qox is the first MCD-containing enzyme to be synthesized in a catalytically fully competent form by a heterologous host, P. (PMID 12730200)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 5'-O-[(S)-{[(S)-{[(8R)-2-Amino-4-hydroxy-6,7-disulfanyl-8H-pyrano[3,2-g]pteridin-8-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
  • 5'-O-[(S)-{[(S)-{[(8R)-2-Amino-4-hydroxy-6,7-disulphanyl-8H-pyrano[3,2-g]pteridin-8-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
  • 5'-O-[{[({[(5aR,8R,9aR)-2-amino-4-oxo-6,7-disulfanyl-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl}oxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
  • 5'-O-[{[({[(5aR,8R,9aR)-2-amino-4-oxo-6,7-disulphanyl-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl}oxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
  • Dtpp-mCDP
  • H2Dtpp-mCDP
  • MCD
  • Molybdopterin cytosine dinucleotide
  • MoO2(OH)Dtpp-mCDP
  • MoO2(OH)Dtpp-mCDP
  • PTERIN CYTOSINE DINUCLEOTIDE
Chemical Formula:C19H23N8O13P2S2
Weight:Average: 697.509
Monoisotopic: 697.030122266
InChI Key:WKSPNQYEWZEMMI-FEFZDOOUSA-K
InChI:InChI=1S/C19H26N8O13P2S2/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14/h1-2,5-6,8,10-11,16-17,23,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H4,21,24,25,26,30)/p-3/t5-,6-,8+,10-,11-,16-,17-/m1/s1
CAS number:Not Available
IUPAC Name:[(5aR,8R,9aR)-2-amino-8-({[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphinato]oxy}methyl)-4-oxo-7-sulfanyl-1H,4H,5H,5aH,8H,9aH,10H-pyrano[3,2-g]pteridin-6-yl]sulfanide
Traditional IUPAC Name:[(5aR,8R,9aR)-2-amino-8-{[({[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphinato)oxy]methyl}-4-oxo-7-sulfanyl-1H,5H,5aH,8H,9aH,10H-pyrano[3,2-g]pteridin-6-yl]sulfanide
SMILES:[H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@@]2([H])O[C@@]3([H])N([H])C4=C(N([H])[C@@]3([H])C([S-])=C2S[H])C(=O)N=C(N([H])[H])N4[H])[C@@]1([H])O[H])N1C([H])=C([H])C(=NC1=O)N([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as molybdopterin dinucleotides. These are a dinucleotide that is made up of a molybdopterin and a purine or pyrimidine base linked to each other through a phosphate chain.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassMolybdopterin dinucleotides
Sub ClassNot Available
Direct ParentMolybdopterin dinucleotides
Alternative Parents
Substituents
  • Molybdopterin dinucleotide
  • Pyrimidine ribonucleoside diphosphate
  • Molybdopterin
  • Pentose phosphate
  • Pentose-5-phosphate
  • Pyranopterin
  • Pterin
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Pteridine
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Aminopyrimidine
  • Pyrimidone
  • Secondary aliphatic/aromatic amine
  • Monosaccharide
  • Phosphoric acid ester
  • Pyrimidine
  • Organic phosphoric acid derivative
  • Pyran
  • Imidolactam
  • Hydropyrimidine
  • Alkyl phosphate
  • Vinylogous amide
  • Heteroaromatic compound
  • Tetrahydrofuran
  • 1,2-diol
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Thioenol
  • Secondary amine
  • Alkylthiol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Organonitrogen compound
  • Organooxygen compound
  • Organosulfur compound
  • Primary amine
  • Alcohol
  • Organic anion
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility7.39 g/LALOGPS
logP-0.59ALOGPS
logP-5.7ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)1.82ChemAxon
pKa (Strongest Basic)3.13ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area317.1 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity158.9 m³·mol⁻¹ChemAxon
Polarizability58.45 ųChemAxon
Number of Rings5ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Cytidine triphosphate + Hydrogen ion + Molybdopterin > Molybdopterin cytosine dinucleotide + Pyrophosphate
Hydrogen ion + molybdenum cofactor + Cytidine triphosphate > Molybdopterin cytosine dinucleotide + Pyrophosphate
molybdenum cofactor + Cytidine triphosphate + Hydrogen ion > Molybdopterin cytosine dinucleotide + Pyrophosphate
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:
  • cytidylyl molybdenum cofactor biosynthesis PWY-6476
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-0000009100-5ffd743798f3825e6ff2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ue9-0113039800-2a8e49e0d5e8fd4ce809View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dl-5940000000-cfead60eff80ef6ac3cbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-0200009000-77e9bce65287d531de4aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0002-3510109100-089a2a17a8174c07a6f7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-000i-9232100000-e2d4834bde7dbc4c4b0fView 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
  • Neumann, M., Mittelstadt, G., Seduk, F., Iobbi-Nivol, C., Leimkuhler, S. (2009). "MocA is a specific cytidylyltransferase involved in molybdopterin cytosine dinucleotide biosynthesis in Escherichia coli." J Biol Chem 284:21891-21898. Pubmed: 19542235
  • Parschat, K., Hauer, B., Kappl, R., Kraft, R., Huttermann, J., Fetzner, S. (2003). "Gene cluster of Arthrobacter ilicis Ru61a involved in the degradation of quinaldine to anthranilate: characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes." J Biol Chem 278:27483-27494. Pubmed: 12730200
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID43955
HMDB IDNot Available
Pubchem Compound ID49792073
Kegg IDNot Available
ChemSpider ID26331972
Wikipedia IDNot Available
BioCyc IDCPD0-1882
EcoCyc IDCPD0-1882

Enzymes

Protein Details
1. Uncharacterized protein ygfJ
General function:
Involved in cytidylyltransferase activity
Specific function:
Specific function unknown
Gene Name:
ygfJ
Uniprot ID:
Q46810
Molecular weight:
21514
Reactions
CTP + molybdenum cofactor = diphosphate + cytidylyl molybdenum cofactor.