MiMeDB: Showing metabocard for Thio-molybdenum cofactor (MMDBc0053807)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-05-16 21:35:24 UTC

Update Date

2024-04-30 20:50:27 UTC

Metabolite ID

MMDBc0053807

Metabolite Identification

Common Name

Thio-molybdenum cofactor

Description

Thio-molybdenum cofactor 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. Thio-molybdenum cofactor is an extremely strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306222023512D          

 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
    6.3451    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
    2.3571   -3.1207    0.0000 S   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


  Mrv1652306222023512D          

 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
    6.3451    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
    2.3571   -3.1207    0.0000 S   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>
MMDBc0053807

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N5O6PS2.Mo.H2O.H2S/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>
DGWROKACVVSIEY-UHFFFAOYSA-N

> <FORMULA>
C10H18MoN5O7PS3

> <MOLECULAR_WEIGHT>
543.39

> <EXACT_MASS>
544.916004383

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
45

> <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 hydrate sulfane

> <ALOGPS_LOGP>
-0.04

> <JCHEM_LOGP>
-1.8514778430814034

> <ALOGPS_LOGS>
-3.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.854304600172498

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1935424585190892

> <JCHEM_PKA_STRONGEST_BASIC>
2.905079388232262

> <JCHEM_POLAR_SURFACE_AREA>
168.51999999999998

> <JCHEM_REFRACTIVITY>
109.779

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.12e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
molybdenum(2+) ion molybdopterin cofactor hydrate sulfane

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  C   UNK     0      -3.445  -1.412   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.112  -0.642   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.556   0.898   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.223   0.898   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.112   0.898   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.778   1.668   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.223  -0.642   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.557   1.668   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.556  -0.642   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.890  -0.642   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       7.224  -1.412   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       1.889   1.668   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       1.889  -1.412   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       4.557  -1.412   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       5.890   0.898   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       4.557   3.208   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -7.446  -2.182   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -6.883  -0.078   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -5.343  -2.745   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -4.779  -0.642   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -0.778  -1.412   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0      -6.113  -1.412   0.000  0.00  0.00           P+0
HETATM   23  S   UNK     0      -3.445   1.668   0.000  0.00  0.00           S+0
HETATM   24  S   UNK     0      -0.778   3.208   0.000  0.00  0.00           S+0
HETATM   25 Mo   UNK     0      11.844   0.000   0.000  0.00  0.00          Mo+2
HETATM   26  O   UNK     0       0.000  -5.825   0.000  0.00  0.00           O+0
HETATM   27  S   UNK     0       4.400  -5.825   0.000  0.00  0.00           S+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

Molecular Formula

C₁₀H₁₈MoN₅O₇PS₃

Average Mass

543.39

Monoisotopic Mass

544.916004383

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 hydrate sulfane

Traditional Name

molybdenum(2+) ion molybdopterin cofactor hydrate sulfane

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C10H14N5O6PS2.Mo.H2O.H2S/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

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

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.21 g/L	ALOGPS
logP	-0.04	ALOGPS
logP	-1.9	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	1.19	ChemAxon
pKa (Strongest Basic)	2.91	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 (1 TMS) - 70eV, Positive	splash10-01ot-9653200000-a23e87d6625a37a9a9d4	2017-10-06	View 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

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Basidiomycota	8	Human feces
Eukaryota/Fungi	Ascomycota	2

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

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

External Links

HMDB ID

HMDB0059640

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

Not Available

METLIN ID

Not Available

PubChem Compound

131769778

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 ]

Showing metabocard for Thio-molybdenum cofactor (MMDBc0053807)

MOL for #<Metabolite:0x00007fec78369068>

3D MOL for #<Metabolite:0x00007fec78369068>

3D SDF for #<Metabolite:0x00007fec78369068>

3D-SDF for #<Metabolite:0x00007fec78369068>

PDB for #<Metabolite:0x00007fec78369068>

3D PDB for #<Metabolite:0x00007fec78369068>

SMILES for #<Metabolite:0x00007fec78369068>

INCHI for #<Metabolite:0x00007fec78369068>

Structure for #<Metabolite:0x00007fec78369068>

3D Structure for #<Metabolite:0x00007fec78369068>