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

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

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
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
MMDBr0019201	2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate	Thiamine monophosphate	Thiamine-phosphate synthase	Synthesis	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

References

Synthesis Reference

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:0x00007f925212e508>

3D MOL for #<Metabolite:0x00007f925212e508>

3D SDF for #<Metabolite:0x00007f925212e508>

3D-SDF for #<Metabolite:0x00007f925212e508>

PDB for #<Metabolite:0x00007f925212e508>

3D PDB for #<Metabolite:0x00007f925212e508>

SMILES for #<Metabolite:0x00007f925212e508>

INCHI for #<Metabolite:0x00007f925212e508>

Structure for #<Metabolite:0x00007f925212e508>

3D Structure for #<Metabolite:0x00007f925212e508>