MiMeDB: Showing metabocard for 6-Hydroxymethyl dihydropterin (MMDBc0031590)

Plant

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:40:32 UTC

Update Date

2022-08-31 18:22:01 UTC

Metabolite ID

MMDBc0031590

Metabolite Identification

Common Name

6-Hydroxymethyl dihydropterin

Description

6-hydroxymethyl dihydropterin is a member of the chemical class known as Pterins and Derivatives. These are polycyclic aromatic compounds containing a pterin moeity, which consist of a pteridine ring bearing a ketone and an amine group to form 2-aminopteridin-4(3H)-one.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D 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>
MMDBc0031590

> <DATABASE_NAME>
MIME

> <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

Synonyms

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

Molecular Formula

C₇H₉N₅O₂

Average Mass

195.1787

Monoisotopic Mass

195.075624557

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

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.47 g/L	ALOGPS
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

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	130	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	153	Pig ; Human feces; Human ; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	66	Human feces; Human ; Human nasopharyngeal swab; Cattle	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	93	Human feces; Human appendix biopsy; Human	Metabolic reconstruction
Bacteria	Fusobacteria	13	Human feces; Human	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	4	Human feces	Unknown
Bacteria	Chlamydiae	4	Human
Bacteria	nah	1
Archaea/Archaea	Euryarchaeota	5
Bacteria	Aquificae	1

Exposure Sources

Food Exposures

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0304227

DrugBank ID

DB02119

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

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

17083

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 6-Hydroxymethyl dihydropterin (MMDBc0031590)

MOL for #<Metabolite:0x0000560be1e4e218>

3D MOL for #<Metabolite:0x0000560be1e4e218>

3D SDF for #<Metabolite:0x0000560be1e4e218>

3D-SDF for #<Metabolite:0x0000560be1e4e218>

PDB for #<Metabolite:0x0000560be1e4e218>

3D PDB for #<Metabolite:0x0000560be1e4e218>

SMILES for #<Metabolite:0x0000560be1e4e218>

INCHI for #<Metabolite:0x0000560be1e4e218>

Structure for #<Metabolite:0x0000560be1e4e218>

3D Structure for #<Metabolite:0x0000560be1e4e218>