MiMeDB: Showing metabocard for 4-Amino-2-methyl-5-phosphomethylpyrimidine (MMDBc0030012)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:50:38 UTC

Update Date

2022-08-31 17:38:39 UTC

Metabolite ID

MMDBc0030012

Metabolite Identification

Common Name

4-Amino-2-methyl-5-phosphomethylpyrimidine

Description

4-amino-2-methyl-5-phosphomethylpyrimidine is a member of the chemical class known as Pyrimidines and Pyrimidine Derivatives. These are compounds containing a pyrimidne ring, which is a six-member aromatic heterocycle which consists of two nitrogen atoms (at positions 1 and 3) and four carbon atoms. Tomato LeTHIC is an Fe-requiring HMP-P synthase involved in thiamine synthesis and regulated by multiple factors. (PMID 21511719 ) 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          

 14 14  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    4.1250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.2539    3.3000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.6039    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    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
 13  3  1  0  0  0  0
 14 10  1  0  0  0  0
 14 11  1  0  0  0  0
 14 12  2  0  0  0  0
 14 13  1  0  0  0  0
M  CHG  2  10  -1  11  -1
M  END
> <DATABASE_ID>
MMDBc0030012

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=NC=C(COP([O-])([O-])=O)C(=N)N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H10N3O4P/c1-4-8-2-5(6(7)9-4)3-13-14(10,11)12/h2H,3H2,1H3,(H2,7,8,9)(H2,10,11,12)/p-2

> <INCHI_KEY>
PKYFHKIYHBRTPI-UHFFFAOYSA-L

> <FORMULA>
C6H8N3O4P

> <MOLECULAR_WEIGHT>
217.122

> <EXACT_MASS>
217.026339907

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
18.247583731001384

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl phosphate

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
-1.9571476964641903

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.3172349614948295

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.621124514300404

> <JCHEM_PKA_STRONGEST_BASIC>
12.199121172419524

> <JCHEM_POLAR_SURFACE_AREA>
120.66000000000001

> <JCHEM_REFRACTIVITY>
56.583000000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.32e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl phosphate

> <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   7.700   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       4.207   6.160   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       1.127   6.160   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       2.667   6.160   0.000  0.00  0.00           P+0
CONECT    1    4                                                            
CONECT    2    5    8                                                       
CONECT    3    5   13                                                       
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   14                                                            
CONECT   11   14                                                            
CONECT   12   14                                                            
CONECT   13    3   14                                                       
CONECT   14   10   11   12   13                                             
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

Synonyms

Value	Source
4-Amino-2-methyl-5-(phosphooxymethyl)pyrimidine	ChEBI
4-Amino-2-methyl-5-phosphonatooxymethylpyrimidine	ChEBI
4-Amino-2-methyl-5-phosphonatooxymethylpyrimidine dianion	ChEBI
4-amino-2-Methyl-5-(phosphonooxymethyl)pyrimidine	ChEBI

Molecular Formula

C₆H₈N₃O₄P

Average Mass

217.122

Monoisotopic Mass

217.026339907

IUPAC Name

(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl phosphate

Traditional Name

(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl phosphate

CAS Registry Number

Not Available

SMILES

CC1=NC=C(COP([O-])([O-])=O)C(=N)N1

InChI Identifier

InChI=1S/C6H10N3O4P/c1-4-8-2-5(6(7)9-4)3-13-14(10,11)12/h2H,3H2,1H3,(H2,7,8,9)(H2,10,11,12)/p-2

InChI Key

PKYFHKIYHBRTPI-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminopyrimidines and derivatives. These are organic compounds containing an amino group attached to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Aminopyrimidines and derivatives

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:58354 )
a small molecule (AMINO-HYDROXYMETHYL-METHYL-PYR-P )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.32 g/L	ALOGPS
logP	-0.59	ALOGPS
logP	-2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.62	ChemAxon
pKa (Strongest Basic)	12.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	120.66 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	56.58 m³·mol⁻¹	ChemAxon
Polarizability	18.25 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

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0007466	4-Amino-5-hydroxymethyl-2-methylpyrimidine	4-Amino-2-methyl-5-phosphomethylpyrimidine	Not Available	VMH	30371894
MMDBr0007531	4-Amino-2-methyl-5-phosphomethylpyrimidine	2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate	Not Available	VMH	30371894
MMDBr0008043	5-Aminoimidazole ribonucleotide	4-Amino-2-methyl-5-phosphomethylpyrimidine	Not Available	VMH	30371894

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	11	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool; Cattle ; Rat ; Turkey ; Dog	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	333	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	394	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool; Cattle ; Rat ; Turkey ; Dog	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	11	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	Actinobacteria	111	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	107	Human feces; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	5	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	18	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	21	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque; Human saliva	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	3	Human feces; Human saliva	Unknown
Bacteria/Eubacteria	Aquificae	1
Bacteria/Eubacteria	Cyanobacteria	35	Human
Archaea/Archaea	Euryarchaeota	26		Metabolic reconstruction
Bacteria/Eubacteria	Thermotogae	5
Bacteria/Eubacteria	Chlorobi	9
Bacteria/Eubacteria	Chloroflexi	3
Bacteria/Eubacteria	Deinococcus-thermus	4
Archaea/Archaea	Crenarchaeota	8		Metabolic reconstruction
Bacteria/Eubacteria	Acidobacteria	1
Bacteria	nah	1
Bacteria/Eubacteria	Nitrospirae	1

Exposure Sources

Source Type	Activity	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

HMDB0304169

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030485

KNApSAcK ID

C00007607

Chemspider ID

24785567

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

58354

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 4-Amino-2-methyl-5-phosphomethylpyrimidine (MMDBc0030012)

MOL for #<Metabolite:0x00007f3e34f188e8>

3D MOL for #<Metabolite:0x00007f3e34f188e8>

3D SDF for #<Metabolite:0x00007f3e34f188e8>

3D-SDF for #<Metabolite:0x00007f3e34f188e8>

PDB for #<Metabolite:0x00007f3e34f188e8>

3D PDB for #<Metabolite:0x00007f3e34f188e8>

SMILES for #<Metabolite:0x00007f3e34f188e8>

INCHI for #<Metabolite:0x00007f3e34f188e8>

Structure for #<Metabolite:0x00007f3e34f188e8>

3D Structure for #<Metabolite:0x00007f3e34f188e8>