MiMeDB: Showing metabocard for 4-amino-2-methyl-5-diphosphomethylpyrimidine (MMDBc0032923)

Microbial

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:27:31 UTC

Update Date

2022-08-31 21:48:38 UTC

Metabolite ID

MMDBc0032923

Metabolite Identification

Common Name

4-amino-2-methyl-5-diphosphomethylpyrimidine

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304202017172D          

 18 18  0  0  0  0            999 V2000
 9999.4930 9999.5975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7787 9999.1849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.0639 9999.5975    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9997.3492 9999.1849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.477710000.3112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.652410000.3112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4930 9997.9463    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.6343 9999.5975    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
 9997.046110000.3112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.9155 9999.1828    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.220610000.3112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.3521 9997.9463    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.9239 9999.5973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.2095 9999.1848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.2095 9998.3598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.9239 9997.9473    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10001.6383 9998.3598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.6383 9999.1848    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  2  0  0  0  0
  3  6  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 17 18  2  0  0  0  0
 18 13  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
  1 14  1  0  0  0  0
 15  7  1  0  0  0  0
 17 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032923

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=NC=C(COP(O)(=O)OP(O)(O)=O)C(N)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H11N3O7P2/c1-4-8-2-5(6(7)9-4)3-15-18(13,14)16-17(10,11)12/h2H,3H2,1H3,(H,13,14)(H2,7,8,9)(H2,10,11,12)

> <INCHI_KEY>
AGQJQCFEPUVXNK-UHFFFAOYSA-N

> <FORMULA>
C6H11N3O7P2

> <MOLECULAR_WEIGHT>
299.115

> <EXACT_MASS>
299.007222745

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
23.48431432022145

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({hydroxy[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methoxy]phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
-2.3882973783585157

> <ALOGPS_LOGS>
-1.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.3174428510223133

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.6101858140652507

> <JCHEM_PKA_STRONGEST_BASIC>
1.7078904884347232

> <JCHEM_POLAR_SURFACE_AREA>
161.53

> <JCHEM_REFRACTIVITY>
69.6993

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[hydroxy((4-imino-2-methyl-3H-pyrimidin-5-yl)methoxy)phosphoryl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0    8665.7208665.915   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8664.3878665.145   0.000  0.00  0.00           O+0
HETATM    3  P   UNK     0    8663.0538665.915   0.000  0.00  0.00           P+0
HETATM    4  O   UNK     0    8661.7188665.145   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8663.8258667.248   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8662.2848667.248   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0    8665.7208662.833   0.000  0.00  0.00           N+0
HETATM    8  P   UNK     0    8660.3848665.915   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0    8661.1538667.248   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8659.0428665.141   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8659.6128667.248   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0    8671.0578662.833   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8668.3918665.915   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8667.0588665.145   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8667.0588663.605   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0    8668.3918662.835   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0    8669.7258663.605   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0    8669.7258665.145   0.000  0.00  0.00           N+0
CONECT    1    2   14                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3    8                                                       
CONECT    5    3                                                            
CONECT    6    3                                                            
CONECT    7   15                                                            
CONECT    8    4    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12   17                                                            
CONECT   13   14   18                                                       
CONECT   14   13   15    1                                                  
CONECT   15   14   16    7                                                  
CONECT   16   15   17                                                       
CONECT   17   18   16   12                                                  
CONECT   18   17   13                                                       
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Value	Source
(4-Amino-2-methylpyrimidin-5-yl)methyl diphosphate	ChEBI
2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate	ChEBI
4-Amino-2-methyl-5-(diphosphooxymethyl)pyrimidine	Kegg
(4-Amino-2-methylpyrimidin-5-yl)methyl diphosphoric acid	Generator
2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphoric acid	Generator
4-amino-2-Methyl-5-diphosphomethylpyrimidine	ChEBI

Molecular Formula

C₆H₁₁N₃O₇P₂

Average Mass

299.115

Monoisotopic Mass

299.007222745

IUPAC Name

({hydroxy[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methoxy]phosphoryl}oxy)phosphonic acid

Traditional Name

[hydroxy((4-imino-2-methyl-3H-pyrimidin-5-yl)methoxy)phosphoryl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

CC1=NC=C(COP(O)(=O)OP(O)(O)=O)C(N)=N1

InChI Identifier

InChI=1S/C6H11N3O7P2/c1-4-8-2-5(6(7)9-4)3-15-18(13,14)16-17(10,11)12/h2H,3H2,1H3,(H,13,14)(H2,7,8,9)(H2,10,11,12)

InChI Key

AGQJQCFEPUVXNK-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organic oxoanionic compounds

Sub Class

Organic pyrophosphates

Direct Parent

Organic pyrophosphates

Alternative Parents

Substituents

Organic pyrophosphate
Aminopyrimidine
Monoalkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Imidolactam
Heteroaromatic compound
Azacycle
Organoheterocyclic compound
Amine
Primary amine
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:16629 )
alkyl diphosphate (CHEBI:16629 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.42 g/L	ALOGPS
logP	-0.59	ALOGPS
logP	-2.4	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	2.61	ChemAxon
pKa (Strongest Basic)	1.71	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	161.53 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	69.7 m³·mol⁻¹	ChemAxon
Polarizability	23.48 Å³	ChemAxon
Number of Rings	1	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	splash10-00mk-9650000000-08bf434ea88992a9a4c2	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fk9-1985000000-3a09f9d4629fc67167b4	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-2910000000-519c49a9a42eb58dbf1e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-8920000000-df2ebfff455ef698c727	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0590000000-b75372b224114b47dc78	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9520000000-644ea3121149c231dadd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-2a0a63f471fc524aa92f	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	534.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	470.4
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	48.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	250.1
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	300.0
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	284.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	403.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	857.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	788.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	163.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	395.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	165.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	29.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	614.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	767.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	64.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	275.4
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	678.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	596.0

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_1	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O)C(N)=N1	standard non polar	2025-10-24	1932.37
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_2	CC1=NC=C(COP(=O)(O)OP(=O)(O)O[Si](C)(C)C)C(N)=N1	standard non polar	2025-10-24	2240.2
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_3	CC1=NC=C(COP(=O)(O)OP(=O)(O)O)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	2035.23
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_4	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C)C(N)=N1	standard non polar	2025-10-24	3077.69
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_5	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	2031.7
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_6	CC1=NC=C(COP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N)=N1	standard non polar	2025-10-24	1692.25
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_7	CC1=NC=C(COP(=O)(O)OP(=O)(O)O[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	2031.29
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_8	CC1=NC=C(COP(=O)(O)OP(=O)(O)O)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	1710.6
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_9	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N)=N1	standard non polar	2025-10-24	2610.62
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_10	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	1506.46
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_11	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	1758.0
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_12	CC1=NC=C(COP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	2211.12
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_13	CC1=NC=C(COP(=O)(O)OP(=O)(O)O[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	1487.19
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_14	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard non polar	2025-10-24	2728.62
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_15	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	2461.94
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_16	CC1=NC=C(COP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	3135.03
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_17	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard non polar	2025-10-24	1864.47
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_1	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O)C(N)=N1	standard polar	2025-10-24	2021.65
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_2	CC1=NC=C(COP(=O)(O)OP(=O)(O)O[Si](C)(C)C)C(N)=N1	standard polar	2025-10-24	2217.4
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_3	CC1=NC=C(COP(=O)(O)OP(=O)(O)O)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	2207.31
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_4	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C)C(N)=N1	standard polar	2025-10-24	2279.33
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_5	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	1965.1
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_6	CC1=NC=C(COP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N)=N1	standard polar	2025-10-24	2816.49
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_7	CC1=NC=C(COP(=O)(O)OP(=O)(O)O[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	2150.04
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_8	CC1=NC=C(COP(=O)(O)OP(=O)(O)O)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	2444.42
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_9	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N)=N1	standard polar	2025-10-24	2179.03
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_10	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	2199.38
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_11	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	2169.54
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_12	CC1=NC=C(COP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	2457.05
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_13	CC1=NC=C(COP(=O)(O)OP(=O)(O)O[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	2633.24
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_14	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N[Si](C)(C)C)=N1	standard polar	2025-10-24	2204.97
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_15	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O)O[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	1693.0
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_16	CC1=NC=C(COP(=O)(O)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	1798.55
Gas Chromatography	4-amino-2-methyl-5-diphosphomethylpyrimidine_TMS_17	CC1=NC=C(COP(=O)(O[Si](C)(C)C)OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C(N([Si](C)(C)C)[Si](C)(C)C)=N1	standard polar	2025-10-24	1532.6

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

Microbial Pathways

Pathways

Name	SMPDB/PathBank	Species
Thiamin Diphosphate Biosynthesis
Thiamine Pyrophosphate Biosynthesis
Vitamin B1/Thiamine Biosynthesis		Escherichia coli Escherichia coli SMS-3-5 Escherichia coli UTI89 Escherichia coli SE11 Escherichia coli CFT073 Bacillus subtilis Klebsiella pneumoniae Bacillus cereus Streptomyces griseus subsp. griseus NBRC 13350 Bacillus amyloliquefaciens Staphylococcus aureus Acidaminococcus fermentans DSM 20731 Acidaminococcus intestini RyC-MR95 Akkermansia muciniphila ATCC BAA-835 Alistipes finegoldii DSM 17242 Bacillus cereus AH187 (F4810/72) Bacillus halodurans C-125 Alkalihalobacillus pseudofirmus OF4 Bacteroides caccae Bacteroides cellulosilyticus Bacteroides eggerthii Bacteroides fragilis Bacteroides fragilis 638R Bacteroides fragilis YCH46 Bacteroides ovatus Bacteroides stercoris Bacteroides stercoris ATCC 43183 Bacteroides thetaiotaomicron Bacteroides thetaiotaomicron VPI-5482 Bacteroides vulgatus Bacteroides xylanisolvens XB1A Bifidobacterium Bifidum Bifidobacterium adolescentis Bifidobacterium adolescentis ATCC 15703 Bifidobacterium bifidum BGN4 Bifidobacterium bifidum PRL2010 Bifidobacterium longum subsp. longum JDM301 Bifidobacterium thermophilum RBL67 Brevibacillus brevis NBRC 100599 Clostridium sticklandii Dysgonomonas gadei ATCC BAA-286 Enterococcus faecalis Odoribacter splanchnicus DSM 20712 Parabacteroides distasonis Parabacteroides distasonis ATCC 8503 Parabacteroides goldsteinii dnLKV18 Porphyromonas gingivalis ATCC 33277 Spirochaeta thermophila Thermus thermophilus Burkholderia cepacia Bradyrhizobium japonicum Chromobacterium violaceum Citrobacter koseri Proteus mirabilis Shigella boydii Shigella dysenteriae Shigella flexneri Shigella sonnei Aeromonas hydrophila Vibrio vulnificus Bacteroides uniformis Fusobacterium ulcerans Desulfovibrio salexigens Capnocytophaga ochracea Capnocytophaga sputigena Staphylococcus epidermidis Bacillus licheniformis Priestia megaterium Bacillus mycoides Bacillus pumilus Bacillus thuringiensis Clostridium butyricum Bifidobacterium angulatum Corynebacterium glutamicum Thermotoga neapolitana Bifidobacterium pseudocatenulatum Staphylococcus lugdunensis Staphylococcus saprophyticus Caldicellulosiruptor bescii Thiobacillus denitrificans Stenotrophomonas maltophilia Actinosynnema mirum Caldicellulosiruptor saccharolyticus Brachyspira pilosicoli Enterobacter cancerogenus Bacillus clausii Bacillus pseudofirmus Peptacetobacter hiranonis Burkholderia cenocepacia Actinomyces urogenitalis Pelotomaculum thermopropionicum Citrobacter youngae Marvinbryantia formatexigens Bacteroides massiliensis Escherichia albertii Bacteroides nordii Bacteroides plebeius Phocaeicola coprocola Bacteroides pyogenes Bacteroides intestinalis Bacteroides salanitronis Bacteroides fluxus Bacteroides oleiciplenus Bacteroides faecis Alistipes finegoldii Bacteroides helcogenes Bacteroides xylanisolvens Bifidobacterium catenulatum Dysgonomonas gadei Klebsiella variicola Odoribacter splanchnicus Parabacteroides goldsteinii Barnesiella intestinihominis Actinobacillus pleuropneumoniae serovar 3 str. JL03 Actinobacillus pleuropneumoniae serovar 7 str. AP76 Aeromonas hydrophila subsp. hydrophila ATCC 7966 Bacillus cereus ATCC 10987 Bacillus megaterium QM B1551 Bacillus thuringiensis serovar konkukian str. 97-27 Bacillus licheniformis ATCC 14580 Bacillus clausii KSM-K16 Bacillus amyloliquefaciens FZB42 Bacillus pumilus SAFR-032 Bacillus cereus B4264 Bacillus cereus AH820 Bacillus cereus G9842 Bacillus cereus Q1 Priestia megaterium DSM 319 Bacillus subtilis subsp. spizizenii str. W23 Bacillus amyloliquefaciens DSM 7 Capnocytophaga ochracea DSM 7271 Citrobacter koseri ATCC BAA-895 Clostridium sticklandii DSM 519 Dyadobacter fermentans DSM 18053 Escherichia coli APEC O1 Escherichia coli E24377A Escherichia coli O127:H6 str. E2348/69 Escherichia coli UMN026 Escherichia fergusonii ATCC 35469 Escherichia coli ED1a Escherichia coli IAI39 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 Lysinibacillus sphaericus C3-41 Escherichia coli 042 Edwardsiella tarda FL6-60 Porphyromonas gingivalis W83 Proteus mirabilis HI4320 Rhodococcus erythropolis PR4 Shigella sonnei Ss046 Shigella flexneri 5 str. 8401 Staphylococcus aureus subsp. aureus Mu50 Staphylococcus aureus subsp. aureus COL Staphylococcus epidermidis RP62A Staphylococcus epidermidis ATCC 12228 Staphylococcus haemolyticus JCSC1435 Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 Staphylococcus aureus subsp. aureus NCTC 8325 Stenotrophomonas maltophilia K279a Stenotrophomonas maltophilia R551-3 Vibrio parahaemolyticus RIMD 2210633 Yersinia enterocolitica subsp. enterocolitica 8081 Yersinia pseudotuberculosis IP 31758 Bacteroides cellulosilyticus DSM 14838 Bacteroides eggerthii 1_2_48FAA Bacteroides fluxus YIT 12057 Bacteroides graminisolvens Bacteroides graminisolvens DSM 19988 = JCM 15093 Bacteroides intestinalis DSM 17393 Bacteroides nordii CL02T12C05 Bacteroides oleiciplenus YIT 12058 Bacteroides ovatus ATCC 8483 Bacteroides pyogenes DSM 20611 = JCM 6294 Bacteroides uniformis ATCC 8492 Bacteroides xylanisolvens SD CC 1b Bacteroides sp. 1_1_14 Bacteroides sp. 1_1_30 Bacteroides sp. 2_1_22 Bacteroides sp. 2_2_4 Bacteroides sp. D2 Bacteroides sp. D20 Bacteroides sp. D22 Barnesiella intestinihominis YIT 11860 Butyricimonas virosa Odoribacter laneus YIT 12061 Paraprevotella clara YIT 11840 Paraprevotella xylaniphila YIT 11841 Prevotella bivia DSM 20514 Prevotella oralis ATCC 33269 Prevotella salivae DSM 15606 Prevotella timonensis CRIS 5C-B1 Parabacteroides johnsonii DSM 18315 Parabacteroides sp. D13 Tannerella forsythia Bacteroides coprophilus DSM 18228 = JCM 13818 Bacteroides dorei DSM 17855 Cetobacterium somerae ATCC BAA-474 Bradyrhizobium elkanii Burkholderia cepacia GG4 Aeromonas caviae Aeromonas media Aeromonas veronii Succinatimonas hippei Succinatimonas hippei YIT 12066 Cedecea davisae Cedecea davisae DSM 4568 Citrobacter amalonaticus Citrobacter amalonaticus Y19 Citrobacter freundii Citrobacter youngae ATCC 29220 Escherichia albertii TW07627 Klebsiella aerogenes Trabulsiella guamensis Trabulsiella guamensis ATCC 49490 Edwardsiella tarda Edwardsiella tarda ATCC 23685 Hafnia alvei Hafnia alvei ATCC 51873 Morganella morganii Morganella morganii subsp. morganii KT Providencia rustigianii DSM 4541 Providencia stuartii ATCC 25827 Serratia marcescens subsp. marcescens Db11 Yersinia enterocolitica Yersinia pestis Yersinia pseudotuberculosis Plesiomonas shigelloides 302-73 Actinobacillus pleuropneumoniae Vibrio parahaemolyticus Brachyspira pilosicoli B2904 Acetomicrobium hydrogeniformans Actinomyces urogenitalis DSM 15434 Bifidobacterium stercoris JCM 15918 Bifidobacterium angulatum DSM 20098 = JCM 7096 Bifidobacterium boum Bifidobacterium catenulatum DSM 16992 = JCM 1194 = LMG 11043 Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505 Bifidobacterium thermacidophilum Bifidobacterium thermophilum Corynebacterium tuberculostearicum Corynebacterium tuberculostearicum SK141 Rhodococcus erythropolis Microbacterium oleivorans Cellulosimicrobium cellulans Bacillus altitudinis Bacillus infantis NRRL B-14911 Bacillus firmus DS1 Lysinibacillus sphaericus Aneurinibacillus aneurinilyticus Aneurinibacillus aneurinilyticus ATCC 12856 Clostridium butyricum E4 str. BoNT E BL5262 Flavonifractor plautii ATCC 29863 Pseudoflavonifractor capillosus ATCC 29799 Acidaminococcus intestini Megasphaera elsdenii Corynebacterium glutamicum ATCC 13032 Bacillus cytotoxicus NVH 391-98 Alkaliphilus oremlandii OhILAs Arthrobacter sp. FB24 Bifidobacterium dentium Bd1 Caldicellulosiruptor bescii DSM 6725 Clostridium tetani E88 Clostridium cellulolyticum H10 Corynebacterium glutamicum R Deinococcus geothermalis DSM 11300 Exiguobacterium sibiricum 255-15 Geobacillus kaustophilus HTA426 Geobacillus thermodenitrificans NG80-2 Macrococcus caseolyticus JCSC5402 Meiothermus ruber DSM 1279 Mycobacterium vanbaalenii PYR-1 Mycobacterium abscessus ATCC 19977 Oceanobacillus iheyensis HTE831 Caldicellulosiruptor saccharolyticus DSM 8903 Dictyoglomus turgidum DSM 6724 Thermobaculum terrenum ATCC BAA-798 Pelotomaculum thermopropionicum SI Mycolicibacterium fortuitum subsp. fortuitum DSM 46621 = ATCC 6841 Bacteroides helcogenes P 36-108 Bacteroides salanitronis DSM 18170 Klebsiella aerogenes KCTC 2190 Halanaerobium hydrogeniformans Aeromonas salmonicida subsp. salmonicida A449 Azotobacter vinelandii DJ Brachyspira hyodysenteriae WA1 Brachyspira pilosicoli 95/1000 Burkholderia mallei ATCC 23344 Burkholderia pseudomallei 1710b Burkholderia sp. 383 Burkholderia mallei NCTC 10229 Burkholderia pseudomallei 1106a Burkholderia cenocepacia J2315 Capnocytophaga canimorsus Cc5 Cellulophaga algicola DSM 14237 Clostridium lentocellum DSM 5427 Cellvibrio gilvus ATCC 13127 Citrobacter rodentium ICC168 Cyanothece sp. ATCC 51142 Cyanothece sp. PCC 8801 Desulfitobacterium hafniense Y51 Desulfitobacterium hafniense DCB-2 Desulfovibrio salexigens DSM 2638 Dichelobacter nodosus VCS1703A Dickeya dadantii Ech703 Dickeya dadantii Ech586 Dickeya dadantii 3937 Edwardsiella ictaluri 93-146 Enterobacter sp. 638 Erwinia tasmaniensis Et1/99 Erwinia amylovora CFBP1430 Erwinia billingiae Eb661 Fervidobacterium nodosum Rt17-B1 Gloeobacter violaceus PCC 7421 Heliobacterium modesticaldum Ice1 Klebsiella pneumoniae 342 Kosmotoga olearia TBF 19.5.1 Meiothermus silvanus DSM 9946 Methylobacillus flagellatus KT Methylobacterium extorquens DM4 Methylovorus glucosetrophus SIP3-4 Nostoc sp. PCC 7120 Chromobacterium violaceum ATCC 12472 Thermus thermophilus HB27 Synechococcus sp. JA-2-3B'a(2-13) Alteromonas macleodii str. 'Deep ecotype' Dictyoglomus thermophilum H-6-12 Thermanaerovibrio acidaminovorans DSM 6589 Denitrovibrio acetiphilus DSM 12809 Thermus scotoductus SA-01 Pantoea ananatis LMG 20103 Pectobacterium atrosepticum SCRI1043 Pectobacterium carotovorum subsp. carotovorum PC1 Petrotoga mobilis SJ95 Photorhabdus luminescens subsp. laumondii TTO1 Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949 Psychromonas ingrahamii 37 Rhodopseudomonas palustris CGA009 Rhodopseudomonas palustris HaA2 Rhodopseudomonas palustris BisB5 Salinibacter ruber DSM 13855 Sebaldella termitidis ATCC 33386 Shigella flexneri 2a str. 301 Shigella boydii Sb227 Spirochaeta thermophila DSM 6192 Synechococcus sp. JA-3-3Ab Thermosipho melanesiensis BI429 Thermosipho africanus TCF52B Thermotoga petrophila RKU-1 Thermotoga sp. RQ2 Thermotoga neapolitana DSM 4359 Tolumonas auensis DSM 9187 Treponema brennaborense DSM 12168 Vibrio vulnificus CMCP6 Vibrio vulnificus YJ016 Vibrio splendidus LGP32 Zunongwangia profunda SM-A87 Sphingobacterium paucimobilis HER1398 Klebsiella michiganensis KCTC 1686 Chania multitudinisentens RB-25 Veillonella seminalis ACS-216-V-Col6b

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018459	2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate	Thiamine monophosphate	Thiamine-phosphate synthase	Synthesis	PathBank	31602464
MMDBr0018461	Pyridoxal 5'-phosphate	4-amino-2-methyl-5-diphosphomethylpyrimidine	HMP-PP phosphatase	Dephosphorylation	PathBank	31602464
MMDBr0019200	4-Amino-2-methyl-5-phosphomethylpyrimidine	4-amino-2-methyl-5-diphosphomethylpyrimidine	Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase	Phosphorylation	PathBank	31602464

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	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Other Exposures

Source Type	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00007609

Chemspider ID

Not Available

KEGG Compound ID

C04752

BioCyc ID

AMINO-HYDROXYMETHYL-METHYLPYRIMIDINE-PP

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

217

PDB ID

Not Available

ChEBI ID

16629

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 4-amino-2-methyl-5-diphosphomethylpyrimidine (MMDBc0032923)

MOL for #<Metabolite:0x00007f2dd18e8298>

3D MOL for #<Metabolite:0x00007f2dd18e8298>

3D SDF for #<Metabolite:0x00007f2dd18e8298>

3D-SDF for #<Metabolite:0x00007f2dd18e8298>

PDB for #<Metabolite:0x00007f2dd18e8298>

3D PDB for #<Metabolite:0x00007f2dd18e8298>

SMILES for #<Metabolite:0x00007f2dd18e8298>

INCHI for #<Metabolite:0x00007f2dd18e8298>

Structure for #<Metabolite:0x00007f2dd18e8298>

3D Structure for #<Metabolite:0x00007f2dd18e8298>