MiMeDB: Showing metabocard for 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate (MMDBc0029977)

Microbial

Plant

Animal

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:49:08 UTC

Update Date

2022-08-31 17:38:14 UTC

Metabolite ID

MMDBc0029977

Metabolite Identification

Common Name

2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate

Description

2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate is a member of the chemical class known as Organic Pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. HMP-PP is involved in thiamin biosynthesis. Two redundant genes, THI20 and THI21, of Saccharomyces cerevisiae encode a 2-methyl-4-amino-5-hydroxymethylpyrimidine monophosphate (HMP-P) kinase required for thiamin biosynthesis. Although each isoform independently can synthesize HMP pyrophosphate (HMP-PP) from HMP, there is a marked difference in efficiency between the two proteins. (PMID 15614489 )

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 01211515292D          

 18 18  0  0  0  0            999 V2000
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.3020    5.2520    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.1270    3.8230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    3.3000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.8250    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
  8  2  1  0  0  0  0
  8  4  2  0  0  0  0
  9  4  1  0  0  0  0
  9  6  1  0  0  0  0
 15  3  1  0  0  0  0
 17 10  1  0  0  0  0
 17 11  1  0  0  0  0
 17 12  2  0  0  0  0
 17 16  1  0  0  0  0
 18 13  1  0  0  0  0
 18 14  2  0  0  0  0
 18 15  1  0  0  0  0
 18 16  1  0  0  0  0
M  CHG  3  10  -1  11  -1  13  -1
M  END
> <DATABASE_ID>
MMDBc0029977

> <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)/p-3

> <INCHI_KEY>
AGQJQCFEPUVXNK-UHFFFAOYSA-K

> <FORMULA>
C6H8N3O7P2

> <MOLECULAR_WEIGHT>
296.093

> <EXACT_MASS>
295.985394345

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
22.61241684386724

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl phosphonato]oxy}phosphonate

> <ALOGPS_LOGP>
-0.34

> <JCHEM_LOGP>
-2.8144504901536602

> <ALOGPS_LOGS>
-1.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.9489004794550797

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7379385479278766

> <JCHEM_PKA_STRONGEST_BASIC>
12.188389108509732

> <JCHEM_POLAR_SURFACE_AREA>
170.01999999999998

> <JCHEM_REFRACTIVITY>
66.33420000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.22e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl phosphonato]oxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-JAN-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JAN-15         0                                  
HETATM    1  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.334   2.310   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       2.667  -0.000   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      -2.667   9.240   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0      -0.564   9.804   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0      -2.104   7.136   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.540   6.160   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0      -1.540   6.160   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   7.700   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0      -1.334   8.470   0.000  0.00  0.00           P+0
HETATM   18  P   UNK     0       0.000   6.160   0.000  0.00  0.00           P+0
CONECT    1    4                                                            
CONECT    2    5    8                                                       
CONECT    3    5   15                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2    3    6                                                  
CONECT    6    5    7    9                                                  
CONECT    7    6                                                            
CONECT    8    2    4                                                       
CONECT    9    4    6                                                       
CONECT   10   17                                                            
CONECT   11   17                                                            
CONECT   12   17                                                            
CONECT   13   18                                                            
CONECT   14   18                                                            
CONECT   15    3   18                                                       
CONECT   16   17   18                                                       
CONECT   17   10   11   12   16                                             
CONECT   18   13   14   15   16                                             
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

COMPND    HMDB0304168
HETATM    1  C1  UNL     1      -4.180   1.389   0.462  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.915   0.627   0.388  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.816   1.092   0.994  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.636   0.443   0.961  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.586  -0.740   0.269  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.601  -1.566   0.158  1.00  0.00           C  
HETATM    7  O1  UNL     1       1.765  -1.158   0.707  1.00  0.00           O  
HETATM    8  P1  UNL     1       2.455   0.237   0.135  1.00  0.00           P  
HETATM    9  O2  UNL     1       2.934   1.079   1.294  1.00  0.00           O  
HETATM   10  O3  UNL     1       1.450   1.106  -0.925  1.00  0.00           O1-
HETATM   11  O4  UNL     1       3.865  -0.124  -0.779  1.00  0.00           O  
HETATM   12  P2  UNL     1       5.177   0.788  -0.240  1.00  0.00           P  
HETATM   13  O5  UNL     1       6.445   0.410  -0.926  1.00  0.00           O  
HETATM   14  O6  UNL     1       4.937   2.441  -0.419  1.00  0.00           O1-
HETATM   15  O7  UNL     1       5.382   0.414   1.418  1.00  0.00           O1-
HETATM   16  C6  UNL     1      -1.735  -1.217  -0.359  1.00  0.00           C  
HETATM   17  N2  UNL     1      -1.725  -2.335  -1.022  1.00  0.00           N  
HETATM   18  N3  UNL     1      -2.875  -0.528  -0.289  1.00  0.00           N  
HETATM   19  H1  UNL     1      -4.847   0.835   1.149  1.00  0.00           H  
HETATM   20  H2  UNL     1      -4.649   1.559  -0.532  1.00  0.00           H  
HETATM   21  H3  UNL     1      -4.024   2.398   0.903  1.00  0.00           H  
HETATM   22  H4  UNL     1       0.246   0.848   1.483  1.00  0.00           H  
HETATM   23  H5  UNL     1       0.728  -1.854  -0.933  1.00  0.00           H  
HETATM   24  H6  UNL     1       0.335  -2.554   0.649  1.00  0.00           H  
HETATM   25  H7  UNL     1      -2.572  -2.707  -1.498  1.00  0.00           H  
HETATM   26  H8  UNL     1      -3.758  -0.886  -0.767  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3    3   18
CONECT    3    4
CONECT    4    5    5   22
CONECT    5    6   16
CONECT    6    7   23   24
CONECT    7    8
CONECT    8    9    9   10   11
CONECT   11   12
CONECT   12   13   13   14   15
CONECT   16   17   17   18
CONECT   17   25
CONECT   18   26
END

Synonyms

Value	Source
4-Amino-2-methyl-5-(diphosphooxymethyl)pyrimidine	ChEBI
4-Amino-2-methyl-5-diphosphonatooxymethylpyrimidine trianion	ChEBI
4-amino-2-Methyl-5-(diphosphonooxymethyl)pyrimidine	ChEBI

Molecular Formula

C₆H₈N₃O₇P₂

Average Mass

296.093

Monoisotopic Mass

295.985394345

IUPAC Name

{[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl phosphonato]oxy}phosphonate

Traditional Name

[(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl phosphonato]oxyphosphonate

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)/p-3

InChI Key

AGQJQCFEPUVXNK-UHFFFAOYSA-K

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
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
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:57841 )
a small molecule (AMINO-HYDROXYMETHYL-METHYLPYRIMIDINE-PP )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	12.2 g/L	ALOGPS
logP	-0.34	ALOGPS
logP	-2.8	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	1.74	ChemAxon
pKa (Strongest Basic)	12.19	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	170.02 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	66.33 m³·mol⁻¹	ChemAxon
Polarizability	22.61 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	Deposition Date	View
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)	2025-10-23	227.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	148.0
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	132.7
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	419.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	319.1
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	284.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	926.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	634.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	717.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	191.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	323.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	165.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	80.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	532.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	545.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	57.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	205.0
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1084.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	667.5

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate_TMS_1	CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)[NH]1	standard non polar	2025-10-23	1496.54
Gas Chromatography	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate_TMS_2	CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N)N1[Si](C)(C)C	standard non polar	2025-10-23	2178.07
Gas Chromatography	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate_TMS_3	CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)N1[Si](C)(C)C	standard non polar	2025-10-23	1895.76
Gas Chromatography	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate_TMS_1	CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)[NH]1	standard polar	2025-10-23	2613.75
Gas Chromatography	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate_TMS_2	CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N)N1[Si](C)(C)C	standard polar	2025-10-23	2345.22
Gas Chromatography	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate_TMS_3	CC1=NC=C(COP(=O)([O-])OP(=O)([O-])[O-])C(=N[Si](C)(C)C)N1[Si](C)(C)C	standard polar	2025-10-23	1876.76

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Not Available

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
MMDBr0019943	4-Amino-2-methyl-5-phosphomethylpyrimidine	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate	Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase THI20	Phosphorylation	PathBank	31602464
MMDBr0019945	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate	Thiamine monophosphate	Thiamine biosynthetic bifunctional enzyme	Thiamine biosynthesis	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
Bacteria	Proteobacteria	4	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Cattle ; Turkey ; Chicken	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	398	Human feces; Human pleural fluid plaque; Pig ; Human ; Human subgingival plaque; Human saliva; Catfish ; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	300	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Cattle ; Turkey ; Chicken	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	132	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	110	Human feces; Human ; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	3	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	18	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	2
Bacteria/Eubacteria	Aquificae	3
Bacteria/Eubacteria	Cyanobacteria	14
Archaea/Archaea	Euryarchaeota	24		Metabolic reconstruction
Bacteria/Eubacteria	Thermotogae	1
Archaea/Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Chloroflexi	4
Bacteria/Eubacteria	Chlamydiae	2	Human ; Sheep
Bacteria/Eubacteria	Chlorobi	6
Bacteria/Eubacteria	Deinococcus-thermus	4
Bacteria/Eubacteria	Dictyoglomi	2
Bacteria/Eubacteria	Acidobacteria	1
Bacteria	nah	1

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0304168

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030484

KNApSAcK ID

Not Available

Chemspider ID

24785117

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

57841

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate (MMDBc0029977)

MOL for #<Metabolite:0x00007f2e091932f8>

3D MOL for #<Metabolite:0x00007f2e091932f8>

3D SDF for #<Metabolite:0x00007f2e091932f8>

3D-SDF for #<Metabolite:0x00007f2e091932f8>

PDB for #<Metabolite:0x00007f2e091932f8>

3D PDB for #<Metabolite:0x00007f2e091932f8>

SMILES for #<Metabolite:0x00007f2e091932f8>

INCHI for #<Metabolite:0x00007f2e091932f8>

Structure for #<Metabolite:0x00007f2e091932f8>

3D Structure for #<Metabolite:0x00007f2e091932f8>