MiMeDB: Showing metabocard for thiamine(1+) diphosphate(1-) (MMDBc0033210)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:39:11 UTC

Update Date

2022-08-31 22:29:51 UTC

MiMeDB ID

MMDBc0033210

Metabolite Identification

Common Name

thiamine(1+) diphosphate(1-)

Description

Thiamine pyrophosphate (ThDP) is one of the five known natural thiamine phosphate derivatives. Thiamine (vitamin B1) is the transport form of the vitamin, while the phosphorylated derivatives are the active forms. Thiamine pyrophosphate serves as a cofactor for several enzymes involved primarily in carbohydrate catabolism.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02231215522D          

 26 27  0  0  1  0            999 V2000
   -6.6835    2.7975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8630    2.8837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5274    3.6374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7070    3.7236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2220    3.0562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4016    3.1424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0660    3.8961    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -3.4785    4.6106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9265    5.2237    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1728    4.8881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4583    5.3006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7438    4.8881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0294    5.3006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6851    4.8881    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
    0.2726    4.1737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0976    5.6026    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3996    4.4756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1140    4.8881    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
    2.8285    5.3006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5265    4.1737    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.7015    5.6026    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2590    4.0676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6459    3.5156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5576    2.3025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0727    1.6351    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3781    2.2163    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  1  0  0  0
 14 16  2  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  1  0  0  0
 18 21  2  0  0  0  0
 10 22  2  0  0  0  0
  7 22  1  0  0  0  0
 22 23  1  0  0  0  0
  5 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
  2 26  1  0  0  0  0
M  CHG  2   7   1  20  -1
M  END


  Mrv0541 02231215522D          

 26 27  0  0  1  0            999 V2000
   -6.6835    2.7975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8630    2.8837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5274    3.6374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7070    3.7236    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2220    3.0562    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4016    3.1424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0660    3.8961    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -3.4785    4.6106    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9265    5.2237    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1728    4.8881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4583    5.3006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7438    4.8881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0294    5.3006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6851    4.8881    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
    0.2726    4.1737    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0976    5.6026    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3996    4.4756    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1140    4.8881    0.0000 P   0  0  2  0  0  0  0  0  0  0  0  0
    2.8285    5.3006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5265    4.1737    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.7015    5.6026    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2590    4.0676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6459    3.5156    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5576    2.3025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0727    1.6351    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3781    2.2163    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  1  0  0  0
 14 16  2  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  1  0  0  0
 18 21  2  0  0  0  0
 10 22  2  0  0  0  0
  7 22  1  0  0  0  0
 22 23  1  0  0  0  0
  5 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  2  0  0  0  0
  2 26  1  0  0  0  0
M  CHG  2   7   1  20  -1
M  END
> <DATABASE_ID>
MMDBc0033210

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=C(CCO[P@](O)(=O)O[P@](O)([O-])=O)SC=[N+]1CC1=CN=C(C)N=C1N

> <INCHI_IDENTIFIER>
InChI=1S/C12H18N4O7P2S/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)

> <INCHI_KEY>
AYEKOFBPNLCAJY-UHFFFAOYSA-N

> <FORMULA>
C12H18N4O7P2S

> <MOLECULAR_WEIGHT>
424.306

> <EXACT_MASS>
424.037142664

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
35.85201507296577

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(hydrogen phosphonatooxy)(hydroxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium

> <ALOGPS_LOGP>
-1.21

> <JCHEM_LOGP>
-5.811121942051653

> <ALOGPS_LOGS>
-3.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.1978567042362194

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.778305935861734

> <JCHEM_PKA_STRONGEST_BASIC>
5.534004899065843

> <JCHEM_POLAR_SURFACE_AREA>
171.8

> <JCHEM_REFRACTIVITY>
94.0238

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.72e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiamin diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0     -12.476   5.222   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0     -10.944   5.383   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0     -10.318   6.790   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -8.786   6.951   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -7.881   5.705   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.350   5.866   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -5.723   7.273   0.000  0.00  0.00           N+1
HETATM    8  C   UNK     0      -6.493   8.606   0.000  0.00  0.00           C+0
HETATM    9  S   UNK     0      -5.463   9.751   0.000  0.00  0.00           S+0
HETATM   10  C   UNK     0      -4.056   9.124   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.722   9.894   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.388   9.124   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.055   9.894   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       1.279   9.124   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0       0.509   7.791   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.049  10.458   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.613   8.354   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       3.946   9.124   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0       5.280   9.894   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.716   7.791   0.000  0.00  0.00           O-1
HETATM   21  O   UNK     0       3.176  10.458   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -4.217   7.593   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.072   6.562   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -8.508   4.298   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0      -7.602   3.052   0.000  0.00  0.00           N+0
HETATM   26  N   UNK     0     -10.039   4.137   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   26                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   24                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   22                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   22                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14   18                                                       
CONECT   18   17   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18                                                            
CONECT   22   10    7   23                                                  
CONECT   23   22                                                            
CONECT   24    5   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24    2                                                       
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

Synonyms

Not Available

Chemical Formula

C₁₂H₁₈N₄O₇P₂S

Average Molecular Weight

424.306

Monoisotopic Molecular Weight

424.037142664

IUPAC Name

3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(hydrogen phosphonatooxy)(hydroxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium

Traditional Name

thiamin diphosphate

CAS Registry Number

Not Available

SMILES

CC1=C(CCO[P@](O)(=O)O[P@](O)([O-])=O)SC=[N+]1CC1=CN=C(C)N=C1N

InChI Identifier

InChI=1S/C12H18N4O7P2S/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)

InChI Key

AYEKOFBPNLCAJY-UHFFFAOYSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.37 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-5.8	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	1.78	ChemAxon
pKa (Strongest Basic)	5.53	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	171.8 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	94.02 m³·mol⁻¹	ChemAxon
Polarizability	35.85 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-002b-8936000000-119f14d7b717fad84f6b	2017-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-03di-2590000000-3b56b15f83f1eb31bbd6	2017-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0100900000-77873d5d6dd317537d7d	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0aba-7147900000-0079e51a57e998b4c558	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4j-4920000000-6090fb0a45c94831fa87	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0000900000-e1117ba0cbb3b3bfd1a4	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-9200200000-4c89cd71f5a2d5ca1cd5	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004j-9100000000-c1192b7bec0b5f39eacf	2016-09-12	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

Not Available

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
Fungi	Ascomycota	1	Human Feces	Unknown

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

Not Available

References

Synthesis Reference

Not Available

General References

Ramirez-Gaona M, Marcu A, Pon A, Guo AC, Sajed T, Wishart NA, Karu N, Djoumbou Feunang Y, Arndt D, Wishart DS: YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Res. 2017 Jan 4;45(D1):D440-D445. doi: 10.1093/nar/gkw1058. Epub 2016 Nov 28. [PubMed:27899612 ]

Showing metabocard for thiamine(1+) diphosphate(1-) (MMDBc0033210)

MOL for #<Metabolite:0x000055b76e1d0008>

3D MOL for #<Metabolite:0x000055b76e1d0008>

3D SDF for #<Metabolite:0x000055b76e1d0008>

3D-SDF for #<Metabolite:0x000055b76e1d0008>

PDB for #<Metabolite:0x000055b76e1d0008>

3D PDB for #<Metabolite:0x000055b76e1d0008>

SMILES for #<Metabolite:0x000055b76e1d0008>

INCHI for #<Metabolite:0x000055b76e1d0008>

Structure for #<Metabolite:0x000055b76e1d0008>

3D Structure for #<Metabolite:0x000055b76e1d0008>