NP-MRD: Showing NP-Card for 4-amino-2-methyl-5-diphosphomethylpyrimidine (NP0334333)

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Record Information

Version

2.0

Created at

2024-09-09 23:12:29 UTC

Updated at

2024-09-09 23:12:30 UTC

NP-MRD ID

NP0334333

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-amino-2-methyl-5-diphosphomethylpyrimidine

Description

2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate, also known as hmp-pp or 4-amino-5-hydroxymethyl-2-methylpyrimidine-pp, is a member of the class of compounds known as organic pyrophosphates. Organic pyrophosphates are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate is soluble (in water) and a moderately acidic compound (based on its pKa). 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate can be found in a number of food items such as purple laver, japanese pumpkin, parsnip, and cloves, which makes 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate a potential biomarker for the consumption of these food products. 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate may be a unique E.Coli metabolite.

Structure

MOL SDF 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>
NP0334333

> <DATABASE_NAME>
NP-MRD

> <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

View in JSmol

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

Chemical Formula

C₆H₈N₃O₇P₂

Average Mass

296.0930 Da

Monoisotopic Mass

295.98539 Da

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

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB030484

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25245586

PDB ID

Not Available

ChEBI ID

57841

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 4-amino-2-methyl-5-diphosphomethylpyrimidine (NP0334333)

MOL for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)

3D MOL for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)

3D SDF for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)

3D-SDF for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)

PDB for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)

3D PDB for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)

SMILES for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)

INCHI for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)

Structure for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)

3D Structure for NP0334333 (4-amino-2-methyl-5-diphosphomethylpyrimidine)