NP-MRD: Showing NP-Card for 2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine (NP0054992)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-04-28 01:10:27 UTC

Updated at

2022-04-28 01:10:27 UTC

NP-MRD ID

NP0054992

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine

Description

6-Hydroxymethyl-7,8-dihydropterin belongs to the class of organic compounds known as pterins and derivatives. These are polycyclic aromatic compounds containing a pterin moiety, which consist of a pteridine ring bearing a ketone and an amine group to form 2-aminopteridin-4(3H)-one. 6-Hydroxymethyl-7,8-dihydropterin is a strong basic compound (based on its pKa). 6-Hydroxymethyl-7,8-dihydropterin exists in both E. Coli (prokaryote) and yeast (eukaryote). Within yeast, 6-hydroxymethyl-7,8-dihydropterin participates in a number of enzymatic reactions. In particular, glycolaldehyde and 6-hydroxymethyl-7,8-dihydropterin can be biosynthesized from 7,8-dihydroneopterin through its interaction with the enzyme folic acid synthesis. In addition, 6-hydroxymethyl-7,8-dihydropterin can be converted into 6-hydroxymethyl-7,8-dihydropterin diphosphate through its interaction with the enzyme folic acid synthesis. 2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine is found in Arabidopsis thaliana and Trypanosoma brucei. In yeast, 6-hydroxymethyl-7,8-dihydropterin is involved in the metabolic pathway called tetrahydrofolate biosynthesis pathway.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652303082008122D          

 14 15  0  0  0  0            999 V2000
   -1.4289   -1.6500    0.0000 N   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   -1.6500    0.0000 N   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
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 N   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
    0.0000    0.8250    0.0000 O   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  2  1  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  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  2 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0054992

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC2=C(N=C(CO)CN2)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C7H9N5O2/c8-7-11-5-4(6(14)12-7)10-3(2-13)1-9-5/h13H,1-2H2,(H4,8,9,11,12,14)

> <INCHI_KEY>
CQQNNQTXUGLUEV-UHFFFAOYSA-N

> <FORMULA>
C7H9N5O2

> <MOLECULAR_WEIGHT>
195.1787

> <EXACT_MASS>
195.075624557

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
18.400015811514606

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-6-(hydroxymethyl)-3,4,7,8-tetrahydropteridin-4-one

> <ALOGPS_LOGP>
-1.69

> <JCHEM_LOGP>
-1.8859297996666662

> <ALOGPS_LOGS>
-1.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.259137167948449

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.624953086632588

> <JCHEM_PKA_STRONGEST_BASIC>
0.7635096882825214

> <JCHEM_POLAR_SURFACE_AREA>
112.1

> <JCHEM_REFRACTIVITY>
57.856899999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.47e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-6-(hydroxymethyl)-7,8-dihydro-3H-pteridin-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  N   UNK     0      -2.667  -3.080   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       0.000  -3.080   0.000  0.00  0.00           N+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  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       2.667  -3.080   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   14                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   11                                                  
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    7   11                                                       
CONECT   11   10    4                                                       
CONECT   12    5   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    2                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol

Synonyms

Value	Source
2-Amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine	ChEBI
HMDP CPD	MeSH

Chemical Formula

C₇H₉N₅O₂

Average Mass

195.1787 Da

Monoisotopic Mass

195.07562 Da

IUPAC Name

2-amino-6-(hydroxymethyl)-3,4,7,8-tetrahydropteridin-4-one

Traditional Name

2-amino-6-(hydroxymethyl)-7,8-dihydro-3H-pteridin-4-one

CAS Registry Number

Not Available

SMILES

NC1=NC2=C(N=C(CO)CN2)C(=O)N1

InChI Identifier

InChI=1S/C7H9N5O2/c8-7-11-5-4(6(14)12-7)10-3(2-13)1-9-5/h13H,1-2H2,(H4,8,9,11,12,14)

InChI Key

CQQNNQTXUGLUEV-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
Arabidopsis thaliana	Plant	KNApSAcK
Trypanosoma brucei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pterins and derivatives. These are polycyclic aromatic compounds containing a pterin moiety, which consist of a pteridine ring bearing a ketone and an amine group to form 2-aminopteridin-4(3H)-one.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pteridines and derivatives

Sub Class

Pterins and derivatives

Direct Parent

Pterins and derivatives

Alternative Parents

Substituents

Pterin
Secondary aliphatic/aromatic amine
Hydroxypyrimidine
Pyrimidine
Heteroaromatic compound
Ketimine
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Secondary amine
Alcohol
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Primary alcohol
Organooxygen compound
Organonitrogen compound
Imine
Amine
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

dihydropterin (CHEBI:17083 )
a small molecule (AMINO-OH-HYDROXYMETHYL-DIHYDROPTERIDINE )

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	-1.7	ALOGPS
logP	-1.9	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	7.62	ChemAxon
pKa (Strongest Basic)	0.76	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	112.1 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	57.86 m³·mol⁻¹	ChemAxon
Polarizability	18.4 Å³	ChemAxon
Number of Rings	2	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

DB02119

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB030597

KNApSAcK ID

C00007501

Chemspider ID

Not Available

KEGG Compound ID

C01300

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

218

PDB ID

Not Available

ChEBI ID

17083

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine (NP0054992)

MOL for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)

3D MOL for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)

3D SDF for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)

3D-SDF for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)

PDB for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)

3D PDB for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)

SMILES for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)

INCHI for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)

Structure for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)

3D Structure for NP0054992 (2-Amino-4-hydroxy-6-(hydroxymethyl)-7,8-dihydropteridine)