NP-MRD: Showing NP-Card for 4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate (NP0045675)

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Record Information

Version

2.0

Created at

2022-03-17 19:33:48 UTC

Updated at

2022-03-17 19:33:48 UTC

NP-MRD ID

NP0045675

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241212152D          

 19 18  0  0  0  0            999 V2000
   -0.9429    0.5304    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6573    0.1179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6573   -0.7072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9429   -1.1197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2284   -0.7072    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2284    0.1179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4861    0.5304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9429   -1.9447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3718   -1.1196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0863   -0.7071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6292   -0.6481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8042   -0.6481    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8055    0.1769    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8042   -1.4731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9792   -0.6481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1542   -0.6481    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1555    0.1769    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1542   -1.4731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3292   -0.6481    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  2  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  4  8  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
 16 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0045675

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H9N3O.H4O7P2/c1-4-8-2-5(3-10)6(7)9-4;1-8(2,3)7-9(4,5)6/h2,10H,3H2,1H3,(H2,7,8,9);(H2,1,2,3)(H2,4,5,6)

> <INCHI_KEY>
PCFPIDTUHTVMCO-UHFFFAOYSA-N

> <FORMULA>
C6H13N3O8P2

> <MOLECULAR_WEIGHT>
317.1302

> <EXACT_MASS>
317.017787431

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
14.192035181360428

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4-amino-2-methylpyrimidin-5-yl)methanol; (phosphonooxy)phosphonic acid

> <JCHEM_LOGP>
-0.36044671066666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.411032868169844

> <JCHEM_PKA_STRONGEST_BASIC>
6.17188544677804

> <JCHEM_POLAR_SURFACE_AREA>
72.03

> <JCHEM_REFRACTIVITY>
39.176500000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
pyrophosphoric acid; toxopyrimidine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  N   UNK     0      -1.760   0.990   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -3.094   0.220   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.094  -1.320   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.760  -2.090   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.426  -1.320   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -0.426   0.220   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.907   0.990   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -1.760  -3.630   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -4.427  -2.090   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -5.761  -1.320   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0     -12.375  -1.210   0.000  0.00  0.00           O+0
HETATM   12  P   UNK     0     -10.835  -1.210   0.000  0.00  0.00           P+0
HETATM   13  O   UNK     0     -10.837   0.330   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0     -10.835  -2.750   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -9.295  -1.210   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0      -7.755  -1.210   0.000  0.00  0.00           P+0
HETATM   17  O   UNK     0      -7.757   0.330   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -7.755  -2.750   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -6.215  -1.210   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    1    5    7                                                  
CONECT    7    6                                                            
CONECT    8    4                                                            
CONECT    9    3   10                                                       
CONECT   10    9                                                            
CONECT   11   12                                                            
CONECT   12   11   13   14   15                                             
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   12   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

View in JSmol

Synonyms

Value	Source
4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphoric acid	Generator

Chemical Formula

C₆H₁₃N₃O₈P₂

Average Mass

317.1302 Da

Monoisotopic Mass

317.01779 Da

IUPAC Name

(4-amino-2-methylpyrimidin-5-yl)methanol; (phosphonooxy)phosphonic acid

Traditional Name

pyrophosphoric acid; toxopyrimidine

CAS Registry Number

Not Available

SMILES

OP(O)(=O)OP(O)(O)=O.CC1=NC=C(CO)C(N)=N1

InChI Identifier

InChI=1S/C6H9N3O.H4O7P2/c1-4-8-2-5(3-10)6(7)9-4;1-8(2,3)7-9(4,5)6/h2,10H,3H2,1H3,(H2,7,8,9);(H2,1,2,3)(H2,4,5,6)

InChI Key

PCFPIDTUHTVMCO-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Brassica napus	FooDB	KNAPSACK

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
Pyrimidine
Imidolactam
Heteroaromatic compound
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Aromatic alcohol
Amine
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	-0.36	ChemAxon
pKa (Strongest Acidic)	14.41	ChemAxon
pKa (Strongest Basic)	6.17	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	72.03 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	39.18 m³·mol⁻¹	ChemAxon
Polarizability	14.19 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

FDB001623

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

22290169

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate (NP0045675)

MOL for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)

3D MOL for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)

3D SDF for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)

3D-SDF for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)

PDB for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)

3D PDB for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)

SMILES for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)

INCHI for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)

Structure for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)

3D Structure for NP0045675 (4-Amino-5-hydroxymethyl-2-methylpyrimidine diphosphate)