MiMeDB: Showing metabocard for 4-amino-5-phosphonooxymethyl-2-methylpyrimidine (MMDBc0031750)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:47:43 UTC

Update Date

2024-04-30 19:51:53 UTC

Metabolite ID

MMDBc0031750

Metabolite Identification

Common Name

4-amino-5-phosphonooxymethyl-2-methylpyrimidine

Description

An aminopyrimidine that is pyrimidine in which the hydrogens at positions 2, 4, and 5 are replaced by methyl, amino, and hydroxymethyl substituents, respectively

Structure

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

Structure #1
  Mrv0541 02241206592D          

 14 14  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    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
    0.7145    1.2375    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  2  5  2  0  0  0  0
  2  8  1  0  0  0  0
  3  5  1  0  0  0  0
  3 13  1  0  0  0  0
  4  8  2  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  9  1  0  0  0  0
 10 14  1  0  0  0  0
 11 14  1  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031750

> <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)

> <INCHI_KEY>
PKYFHKIYHBRTPI-UHFFFAOYSA-N

> <FORMULA>
C6H10N3O4P

> <MOLECULAR_WEIGHT>
219.1351

> <EXACT_MASS>
219.040892335

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
18.825297834219008

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methoxy]phosphonic acid

> <ALOGPS_LOGP>
-1.06

> <JCHEM_LOGP>
-1.8085892731666544

> <ALOGPS_LOGS>
-2.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.613949242433612

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6236681682608518

> <JCHEM_PKA_STRONGEST_BASIC>
7.588072702550217

> <JCHEM_POLAR_SURFACE_AREA>
115.00000000000001

> <JCHEM_REFRACTIVITY>
58.8264

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.57e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       0.000  -6.160   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.540  -4.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540  -4.620   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       0.000  -4.620   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-hydroxymethylpyrimidine phosphate	ChEBI
4-Amino-2-methyl-5-phosphonooxymethylpyrimidine	ChEBI
4-Amino-5-phosphomethyl-2-methylpyrimidine	ChEBI
HMP-p	ChEBI
(4-Amino-2-methylpyrimidin-5-yl)methyl phosphate	Kegg
4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphate	Kegg
4-Amino-2-methyl-5-hydroxymethylpyrimidine phosphoric acid	Generator
(4-Amino-2-methylpyrimidin-5-yl)methyl phosphoric acid	Generator
4-Amino-5-hydroxymethyl-2-methylpyrimidine phosphoric acid	Generator
4-Amino-2-methyl-5-phosphomethylpyrimidine	ChEBI

Molecular Formula

C₆H₁₀N₃O₄P

Average Mass

219.1351

Monoisotopic Mass

219.040892335

IUPAC Name

[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methoxy]phosphonic acid

Traditional Name

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

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)

InChI Key

PKYFHKIYHBRTPI-UHFFFAOYSA-N

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

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

aminopyrimidine (CHEBI:18032 )
monoalkyl phosphate (CHEBI:18032 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.76 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-1.8	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	1.62	ChemAxon
pKa (Strongest Basic)	7.59	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	115 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	58.83 m³·mol⁻¹	ChemAxon
Polarizability	18.83 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	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-006t-9620000000-67208cb5c399d7eb0927	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-1690000000-b4b286e97e3c3859ded5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00di-2900000000-ef20fcb4606f47d76648	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00ea-9400000000-23f2dc587b8ee21085af	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-016s-9080000000-bb863e533b4baa6368fd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-f35dbb3f524d9e7e08e0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-04a487a0ef46589c29a0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-0490000000-d0df918acbe4ba0a1686	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00e9-8900000000-4224a9cd25055b1596c1	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0560-9200000000-d4f98d693c874da458ad	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9010000000-28b8f8a4523c0b4ca1a8	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-12	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

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

Not Available

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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Blood	Detected but not Quantified						Not Specified	Not Specified	Normal	HMDB	31557052

External Links

HMDB ID

HMDB0243613

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00007607

Chemspider ID

211

KEGG Compound ID

C04556

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

18032

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 4-amino-5-phosphonooxymethyl-2-methylpyrimidine (MMDBc0031750)

MOL for #<Metabolite:0x00007f46eddae338>

3D MOL for #<Metabolite:0x00007f46eddae338>

3D SDF for #<Metabolite:0x00007f46eddae338>

3D-SDF for #<Metabolite:0x00007f46eddae338>

PDB for #<Metabolite:0x00007f46eddae338>

3D PDB for #<Metabolite:0x00007f46eddae338>

SMILES for #<Metabolite:0x00007f46eddae338>

INCHI for #<Metabolite:0x00007f46eddae338>

Structure for #<Metabolite:0x00007f46eddae338>

3D Structure for #<Metabolite:0x00007f46eddae338>