MiMeDB: Showing metabocard for molybdenum cofactor (MMDBc0031162)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 00:37:51 UTC

Update Date

2022-08-31 17:59:01 UTC

MiMeDB ID

MMDBc0031162

Metabolite Identification

Common Name

molybdenum cofactor

Description

Molybdenum cofactor is a cofactor required for the activity of enzymes such as sulfite oxidase, xanthine oxidoreductase, and aldehyde oxidase. It is a coordination complex formed between molybdopterin (which, despite the name, does not contain molybdenum) and an oxide of molybdenum. Molybdenum-containing enzymes catalyze basic metabolic reactions in the nitrogen, sulfur, and carbon cycles. With the exception of the nitrogenase cofactor, molybdenum is incorporated into proteins as the molybdenum cofactor that contains a mononuclear molybdenum atom coordinated to the sulfur atoms of a pterin derivative named molybdopterin. Certain microorganisms can also utilize tungsten in a similar fashion. Molybdenum-cofactor-containing enzymes catalyze the transfer of an oxygen atom, ultimately derived from or incorporated into water, to or from a substrate in a two-electron redox reaction.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10101211232D          

 27 26  0  0  0  0            999 V2000
   -1.8457   -0.7563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1312   -0.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2977    0.4812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7266    0.4813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1312    0.4813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4168    0.8938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7266   -0.3437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4411    0.8937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2977   -0.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1556   -0.3437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8701   -0.7562    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0122    0.8938    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0122   -0.7563    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4411   -0.7563    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1556    0.4813    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4411    1.7188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9891   -1.1688    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6872   -0.0418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8622   -1.4707    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5602   -0.3438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4168   -0.7563    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2747   -0.7563    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8457    0.8938    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4168    1.7188    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.2272    0.0000    0.0000 Mo  0  2  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.1207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2393   -3.1207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  2  0  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
  9  3  1  0  0  0  0
 11 10  2  0  0  0  0
 12  3  1  0  0  0  0
 12  4  1  0  0  0  0
 13  7  1  0  0  0  0
 13  9  1  0  0  0  0
 14  7  1  0  0  0  0
 14 10  1  0  0  0  0
 15  8  2  0  0  0  0
 15 10  1  0  0  0  0
 16  8  1  0  0  0  0
 20  1  1  0  0  0  0
 21  2  1  0  0  0  0
 21  9  1  0  0  0  0
 22 17  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  2  0  0  0  0
 22 20  1  0  0  0  0
 23  5  1  0  0  0  0
 24  6  1  0  0  0  0
M  CHG  1  25   2
M  END


  Mrv0541 10101211232D          

 27 26  0  0  0  0            999 V2000
   -1.8457   -0.7563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1312   -0.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2977    0.4812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7266    0.4813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1312    0.4813    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4168    0.8938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7266   -0.3437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4411    0.8937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2977   -0.3438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1556   -0.3437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8701   -0.7562    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0122    0.8938    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0122   -0.7563    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4411   -0.7563    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1556    0.4813    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4411    1.7188    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9891   -1.1688    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6872   -0.0418    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8622   -1.4707    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5602   -0.3438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4168   -0.7563    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2747   -0.7563    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8457    0.8938    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4168    1.7188    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.2272    0.0000    0.0000 Mo  0  2  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.1207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2393   -3.1207    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  6  5  2  0  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
  9  3  1  0  0  0  0
 11 10  2  0  0  0  0
 12  3  1  0  0  0  0
 12  4  1  0  0  0  0
 13  7  1  0  0  0  0
 13  9  1  0  0  0  0
 14  7  1  0  0  0  0
 14 10  1  0  0  0  0
 15  8  2  0  0  0  0
 15 10  1  0  0  0  0
 16  8  1  0  0  0  0
 20  1  1  0  0  0  0
 21  2  1  0  0  0  0
 21  9  1  0  0  0  0
 22 17  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  2  0  0  0  0
 22 20  1  0  0  0  0
 23  5  1  0  0  0  0
 24  6  1  0  0  0  0
M  CHG  1  25   2
M  END
> <DATABASE_ID>
MMDBc0031162

> <DATABASE_NAME>
MIME

> <SMILES>
O.O.[Mo++].OC1=NC(=N)NC2=C1NC1C(N2)OC(COP(O)(O)=O)C(S)=C1S

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N5O6PS2.Mo.2H2O/c11-10-14-7-4(8(16)15-10)12-3-6(24)5(23)2(21-9(3)13-7)1-20-22(17,18)19;;;/h2-3,9,12,23-24H,1H2,(H2,17,18,19)(H4,11,13,14,15,16);;2*1H2/q;+2;;

> <INCHI_KEY>
VUKICSJFFDCESC-UHFFFAOYSA-N

> <FORMULA>
C10H18MoN5O8PS2

> <MOLECULAR_WEIGHT>
527.32

> <EXACT_MASS>
528.938848315

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
34.88578439001665

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
molybdenum(2+) ion ({4-hydroxy-2-imino-6,7-disulfanyl-1H,2H,5H,5aH,8H,9aH,10H-pyrano[3,2-g]pteridin-8-yl}methoxy)phosphonic acid dihydrate

> <JCHEM_LOGP>
-4.9764060082650685

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
1.188672302828775

> <JCHEM_PKA_STRONGEST_ACIDIC>
-4.055782166203575

> <JCHEM_PKA_STRONGEST_BASIC>
15.000003628591818

> <JCHEM_POLAR_SURFACE_AREA>
168.51999999999998

> <JCHEM_REFRACTIVITY>
109.779

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
molybdenum(2+) ion molybdopterin cofactor dihydrate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   23  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   24  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   25 Mo   UNK     0       0.000   0.000   0.000  0.00  0.00          Mo+2
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2   20                                                       
CONECT    2    1    5   21                                                  
CONECT    3    6    9   12                                                  
CONECT    4    7    8   12                                                  
CONECT    5    2    6   23                                                  
CONECT    6    3    5   24                                                  
CONECT    7    4   13   14                                                  
CONECT    8    4   15   16                                                  
CONECT    9    3   13   21                                                  
CONECT   10   11   14   15                                                  
CONECT   11   10                                                            
CONECT   12    3    4                                                       
CONECT   13    7    9                                                       
CONECT   14    7   10                                                       
CONECT   15    8   10                                                       
CONECT   16    8                                                            
CONECT   17   22                                                            
CONECT   18   22                                                            
CONECT   19   22                                                            
CONECT   20    1   22                                                       
CONECT   21    2    9                                                       
CONECT   22   17   18   19   20                                             
CONECT   23    5                                                            
CONECT   24    6                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   52    0
END

Synonyms

Not Available

Chemical Formula

C₁₀H₁₈MoN₅O₈PS₂

Average Molecular Weight

527.32

Monoisotopic Molecular Weight

528.938848315

IUPAC Name

molybdenum(2+) ion ({4-hydroxy-2-imino-6,7-disulfanyl-1H,2H,5H,5aH,8H,9aH,10H-pyrano[3,2-g]pteridin-8-yl}methoxy)phosphonic acid dihydrate

Traditional Name

molybdenum(2+) ion molybdopterin cofactor dihydrate

CAS Registry Number

73508-07-3

SMILES

O.O.[Mo++].OC1=NC(=N)NC2=C1NC1C(N2)OC(COP(O)(O)=O)C(S)=C1S

InChI Identifier

InChI=1S/C10H14N5O6PS2.Mo.2H2O/c11-10-14-7-4(8(16)15-10)12-3-6(24)5(23)2(21-9(3)13-7)1-20-22(17,18)19;;;/h2-3,9,12,23-24H,1H2,(H2,17,18,19)(H4,11,13,14,15,16);;2*1H2/q;+2;;

InChI Key

VUKICSJFFDCESC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyranopterins and derivatives. These are pterin derivatives in which a pyran ring is fused either to the pyrimidine ring or the pyrazine ring of the pterin moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pteridines and derivatives

Sub Class

Pterins and derivatives

Direct Parent

Pyranopterins and derivatives

Alternative Parents

Substituents

Pyranopterin
Hydroxypyrimidine
Monoalkyl phosphate
Secondary aliphatic/aromatic amine
Alkyl phosphate
Pyrimidine
Pyran
Phosphoric acid ester
Organic phosphoric acid derivative
Heteroaromatic compound
Oxacycle
Azacycle
Organic transition metal salt
Thioenol
Secondary amine
Alkylthiol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic salt
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Amine
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
logP	-5	ChemAxon
pKa (Strongest Acidic)	-4.1	ChemAxon
pKa (Strongest Basic)	15	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	168.52 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	109.78 m³·mol⁻¹	ChemAxon
Polarizability	34.89 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_5_16) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
	Proteobacteria	127	Human ; Sheep ; Chicken ; Human Feces	Unknown;
	Firmicutes	48	Human Feces; Human ; Cattle
	Aquificae	2
	Chloroflexi	1
	Deinococcus-Thermus	1
	Bacteroidetes	1
Archaea	Euryarchaeota	11
	Actinobacteria	11	Human ; Cattle
	Cyanobacteria	4
	Verrucomicrobia	1
	Planctomycetes	1
NULL	Proteobacteria	1
		1
Archaea		1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Molybdenum cofactor

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for molybdenum cofactor (MMDBc0031162)

MOL for #<Metabolite:0x00007f09200f8310>

3D MOL for #<Metabolite:0x00007f09200f8310>

3D SDF for #<Metabolite:0x00007f09200f8310>

3D-SDF for #<Metabolite:0x00007f09200f8310>

PDB for #<Metabolite:0x00007f09200f8310>

3D PDB for #<Metabolite:0x00007f09200f8310>

SMILES for #<Metabolite:0x00007f09200f8310>

INCHI for #<Metabolite:0x00007f09200f8310>

Structure for #<Metabolite:0x00007f09200f8310>

3D Structure for #<Metabolite:0x00007f09200f8310>