MiMeDB: Showing metabocard for TDP (MMDBc0031794)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:49:34 UTC

Update Date

2024-10-06 21:57:34 UTC

Metabolite ID

MMDBc0031794

Metabolite Identification

Common Name

TDP

Description

Thymidine diphosphate is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside thymidine. TDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase thymine. TDP is produced during the synthesis of LPS via the enzyme 4-alpha-L-fucosyltransferase which catalyzes the reaction TDP-Fuc4NAc + Und-PP-GlcNAc-ManNAcA = TDP + Und-PP-GlcNAc-ManNAcA-Fuc4NAc. This reaction leads to the Lipid III product, which is third lipid-linked intermediate involved in LPS synthesis.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10101211222D          

 27 27  0  0  0  0            999 V2000
   -0.5242    0.5087    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7857    3.2137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0304   -1.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7901   -1.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6423    2.8012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9278    1.5637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5953    0.2538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2604    0.2538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0712    2.8012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6423    1.9762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5153   -0.5308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3568    1.5637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3568    0.7387    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3568    3.2137    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0712    1.9762    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9278    0.7387    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -3.8858   -2.9419    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0683   -1.7895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7335   -2.7594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0093   -0.8728    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1817   -2.5137    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.2750   -1.7795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9160   -1.6070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4009   -2.2744    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0955   -1.6932    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.3403   -0.5308    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.0250    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  8  1  1  0  0  0  0
  9  2  1  0  0  0  0
 10  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  3  1  0  0  0  0
 11  8  2  0  0  0  0
 12 10  1  0  0  0  0
 13 12  2  0  0  0  0
 14  5  1  0  0  0  0
 14  9  2  0  0  0  0
 15  9  1  0  0  0  0
 15 12  1  0  0  0  0
 16  6  1  0  0  0  0
 16  7  2  0  0  0  0
 16  8  1  0  0  0  0
 22  4  1  0  0  0  0
 24 17  2  0  0  0  0
 24 18  1  0  0  0  0
 24 19  1  0  0  0  0
 24 23  1  0  0  0  0
 25 20  2  0  0  0  0
 25 21  1  0  0  0  0
 25 22  1  0  0  0  0
 25 23  1  0  0  0  0
 26  7  1  0  0  0  0
 26 11  1  0  0  0  0
M  CHG  2  16   1  21  -1
M  END


  Mrv0541 10101211222D          

 27 27  0  0  0  0            999 V2000
   -0.5242    0.5087    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7857    3.2137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0304   -1.1983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7901   -1.1120    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6423    2.8012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9278    1.5637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5953    0.2538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2604    0.2538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0712    2.8012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6423    1.9762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5153   -0.5308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3568    1.5637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3568    0.7387    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3568    3.2137    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0712    1.9762    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9278    0.7387    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -3.8858   -2.9419    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0683   -1.7895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7335   -2.7594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0093   -0.8728    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1817   -2.5137    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.2750   -1.7795    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9160   -1.6070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4009   -2.2744    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0955   -1.6932    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.3403   -0.5308    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.0250    0.0000    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  8  1  1  0  0  0  0
  9  2  1  0  0  0  0
 10  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  3  1  0  0  0  0
 11  8  2  0  0  0  0
 12 10  1  0  0  0  0
 13 12  2  0  0  0  0
 14  5  1  0  0  0  0
 14  9  2  0  0  0  0
 15  9  1  0  0  0  0
 15 12  1  0  0  0  0
 16  6  1  0  0  0  0
 16  7  2  0  0  0  0
 16  8  1  0  0  0  0
 22  4  1  0  0  0  0
 24 17  2  0  0  0  0
 24 18  1  0  0  0  0
 24 19  1  0  0  0  0
 24 23  1  0  0  0  0
 25 20  2  0  0  0  0
 25 21  1  0  0  0  0
 25 22  1  0  0  0  0
 25 23  1  0  0  0  0
 26  7  1  0  0  0  0
 26 11  1  0  0  0  0
M  CHG  2  16   1  21  -1
M  END
> <DATABASE_ID>
MMDBc0031794

> <DATABASE_NAME>
MIME

> <SMILES>
Cl.CC1=C(CCOP([O-])(=O)OP(O)(O)=O)SC=[N+]1CC1=CN=C(C)NC1=N

> <INCHI_IDENTIFIER>
InChI=1S/C12H18N4O7P2S.ClH/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13;/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21);1H

> <INCHI_KEY>
YXVCLPJQTZXJLH-UHFFFAOYSA-N

> <FORMULA>
C12H19ClN4O7P2S

> <MOLECULAR_WEIGHT>
460.767

> <EXACT_MASS>
460.013820403

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
36.43026593440044

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]-4-methyl-5-{2-[(phosphono phosphonato)oxy]ethyl}-1,3-thiazol-3-ium hydrochloride

> <JCHEM_LOGP>
-8.199739310236883

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.7934552660550116

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.751126388328636

> <JCHEM_PKA_STRONGEST_BASIC>
6.886687924587707

> <JCHEM_POLAR_SURFACE_AREA>
168.23999999999998

> <JCHEM_REFRACTIVITY>
102.80079999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-[(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl]-4-methyl-5-{2-[(phosphono phosphonato)oxy]ethyl}-1,3-thiazol-3-ium hydrochloride

> <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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+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  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+1
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-1
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   25  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   26  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   27 Cl   UNK     0       0.000   0.000   0.000  0.00  0.00          Cl+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3    4   11                                                       
CONECT    4    3   22                                                       
CONECT    5   10   14                                                       
CONECT    6   10   16                                                       
CONECT    7   16   26                                                       
CONECT    8    1   11   16                                                  
CONECT    9    2   14   15                                                  
CONECT   10    5    6   12                                                  
CONECT   11    3    8   26                                                  
CONECT   12   10   13   15                                                  
CONECT   13   12                                                            
CONECT   14    5    9                                                       
CONECT   15    9   12                                                       
CONECT   16    6    7    8                                                  
CONECT   17   24                                                            
CONECT   18   24                                                            
CONECT   19   24                                                            
CONECT   20   25                                                            
CONECT   21   25                                                            
CONECT   22    4   25                                                       
CONECT   23   24   25                                                       
CONECT   24   17   18   19   23                                             
CONECT   25   20   21   22   23                                             
CONECT   26    7   11                                                       
MASTER        0    0    0    0    0    0    0    0   27    0   54    0
END

Synonyms

Value	Source
3-[(4-Amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium chloride	ChEBI
Cocarboxilasa	ChEBI
Cocarboxylase	ChEBI
Cocarboxylasum	ChEBI
Coenzymate	ChEBI
Thiamine diphosphate chloride	ChEBI
Thiamine pyrophosphate	ChEBI
Thiazolium, 3-((4-amino-2-methyl-5-pyrimidinyl)methyl)-4-methyl-5-(4,6,6-trihydroxy-3,5-dioxa-4,6-diphosphahex-1-yl)-, chloride, p,p'-dioxide	ChEBI
Coenzymic acid	Generator
Thiamine diphosphoric acid chloride	Generator
Thiamine pyrophosphoric acid	Generator
Pyrophosphate, thiamine	MeSH
Berolase	MeSH
Thiamine diphosphate	MeSH

Molecular Formula

C₁₂H₁₉ClN₄O₇P₂S

Average Mass

460.767

Monoisotopic Mass

460.013820403

IUPAC Name

3-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]-4-methyl-5-{2-[(phosphono phosphonato)oxy]ethyl}-1,3-thiazol-3-ium hydrochloride

Traditional Name

3-[(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl]-4-methyl-5-{2-[(phosphono phosphonato)oxy]ethyl}-1,3-thiazol-3-ium hydrochloride

CAS Registry Number

Not Available

SMILES

Cl.CC1=C(CCOP([O-])(=O)OP(O)(O)=O)SC=[N+]1CC1=CN=C(C)NC1=N

InChI Identifier

InChI=1S/C12H18N4O7P2S.ClH/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13;/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21);1H

InChI Key

YXVCLPJQTZXJLH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thiamine phosphates. These are thiamine derivatives in which the hydroxyl group of the ethanol moiety is substituted by a phosphate group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Thiamine phosphates

Alternative Parents

Substituents

Thiamine-phosphate
Organic pyrophosphate
4,5-disubstituted 1,3-thiazole
Aminopyrimidine
Monoalkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Imidolactam
Heteroaromatic compound
Azole
Thiazole
Azacycle
Organic oxygen compound
Organic chloride salt
Organic oxide
Primary amine
Amine
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic zwitterion
Organic salt
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organic chloride salt (CHEBI:18290 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-8.2	ChemAxon
pKa (Strongest Acidic)	1.75	ChemAxon
pKa (Strongest Basic)	6.89	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	168.24 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	102.8 m³·mol⁻¹	ChemAxon
Polarizability	36.43 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria/Eubacteria	Actinobacteria	16	Human ; Cattle

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox

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

DBSALT002497

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

TDP

METLIN ID

Not Available

PubChem Compound

9068

PDB ID

Not Available

ChEBI ID

18290

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 TDP (MMDBc0031794)

MOL for #<Metabolite:0x00007f9231891c30>

3D MOL for #<Metabolite:0x00007f9231891c30>

3D SDF for #<Metabolite:0x00007f9231891c30>

3D-SDF for #<Metabolite:0x00007f9231891c30>

PDB for #<Metabolite:0x00007f9231891c30>

3D PDB for #<Metabolite:0x00007f9231891c30>

SMILES for #<Metabolite:0x00007f9231891c30>

INCHI for #<Metabolite:0x00007f9231891c30>

Structure for #<Metabolite:0x00007f9231891c30>

3D Structure for #<Metabolite:0x00007f9231891c30>