MiMeDB: Showing metabocard for H2-6-Hydroxymethylpterin (MMDBc0009165)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 01:46:13 UTC

Update Date

2022-08-31 06:29:41 UTC

Metabolite ID

MMDBc0009165

Metabolite Identification

Common Name

H2-6-Hydroxymethylpterin

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1652303042020022D          

 22 23  0  0  0  0            999 V2000
   20.6449  -16.1847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.6449  -15.3594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9284  -16.6013    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.3652  -16.6013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9284  -14.9504    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.3615  -14.9392    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.2230  -16.1847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.0855  -16.1885    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.3652  -17.4154    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.2230  -15.3594    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.0818  -15.3557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5140  -16.5899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.7871  -14.9429    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.8086  -16.1772    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9908  -16.1772    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   16.1766  -16.1772    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9945  -15.3594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9908  -16.9914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3588  -16.1772    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   14.5446  -16.1772    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3625  -15.3594    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3588  -16.9914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  6 11  2  0  0  0  0
  7 12  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  2  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 19 22  2  0  0  0  0
  7 10  1  0  0  0  0
  8 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009165

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H11N5O8P2/c8-7-11-5-4(6(13)12-7)10-3(1-9-5)2-19-22(17,18)20-21(14,15)16/h1-2H2,(H,17,18)(H2,14,15,16)(H4,8,9,11,12,13)

> <INCHI_KEY>
FCQGJGLSOWZZON-UHFFFAOYSA-N

> <FORMULA>
C7H11N5O8P2

> <MOLECULAR_WEIGHT>
355.1385

> <EXACT_MASS>
355.008285377

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
27.510605159708383

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({[(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)methoxy](hydroxy)phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
-1.41

> <JCHEM_LOGP>
-2.607077504111404

> <ALOGPS_LOGS>
-1.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.1978473453823777

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7822465904469817

> <JCHEM_PKA_STRONGEST_BASIC>
0.43217034114810493

> <JCHEM_POLAR_SURFACE_AREA>
205.15999999999997

> <JCHEM_REFRACTIVITY>
79.60269999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.13e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2-amino-4-oxo-7,8-dihydro-3H-pteridin-6-yl)methoxy(hydroxy)phosphoryl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAR-20         0                                  
HETATM    1  C   UNK     0      38.537 -30.211   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      38.537 -28.671   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      37.200 -30.989   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      39.882 -30.989   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      37.200 -27.907   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      39.875 -27.887   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      35.883 -30.211   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      41.226 -30.219   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      39.882 -32.509   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      35.883 -28.671   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      41.219 -28.664   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      34.559 -30.968   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      42.536 -27.893   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0      33.243 -30.197   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0      31.716 -30.197   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0      30.196 -30.197   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      31.723 -28.671   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      31.716 -31.717   0.000  0.00  0.00           O+0
HETATM   19  P   UNK     0      28.670 -30.197   0.000  0.00  0.00           P+0
HETATM   20  O   UNK     0      27.150 -30.197   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      28.677 -28.671   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      28.670 -31.717   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8    9                                                  
CONECT    5    2   10                                                       
CONECT    6    2   11                                                       
CONECT    7    3   12   10                                                  
CONECT    8    4   11                                                       
CONECT    9    4                                                            
CONECT   10    5    7                                                       
CONECT   11    6   13    8                                                  
CONECT   12    7   14                                                       
CONECT   13   11                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15   19                                                       
CONECT   17   15                                                            
CONECT   18   15                                                            
CONECT   19   16   20   21   22                                             
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   19                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

Synonyms

Value	Source
2-Amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate	ChEBI
2-Amino-4-hydroxy-6-pyrophosphoryl-methylpteridine	ChEBI
2-Amino-7,8-dihydro-4-hydroxy-6-(diphosphooxymethyl)pteridine	ChEBI
7,8-Dihydropterin pyrophosphate	ChEBI
Pteridine diphosphate	ChEBI
(7,8-Dihydropterin-6-yl)methyl diphosphate	Kegg
2-Amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphoric acid	Generator
7,8-Dihydropterin pyrophosphoric acid	Generator
Pteridine diphosphoric acid	Generator
(7,8-Dihydropterin-6-yl)methyl diphosphoric acid	Generator
(2-Amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphoric acid(3-)	Generator
(2-amino-4-Hydroxy-7,8-dihydropteridin-6-yl)methyl trihydrogen diphosphoric acid	Generator
6-Hydroxymethyl-7,8-dihydropterin diphosphoric acid	Generator

Molecular Formula

C₇H₁₁N₅O₈P₂

Average Mass

355.1385

Monoisotopic Mass

355.008285377

IUPAC Name

({[(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)methoxy](hydroxy)phosphoryl}oxy)phosphonic acid

Traditional Name

[(2-amino-4-oxo-7,8-dihydro-3H-pteridin-6-yl)methoxy(hydroxy)phosphoryl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

NC1=NC2=C(N=C(COP(O)(=O)OP(O)(O)=O)CN2)C(=O)N1

InChI Identifier

InChI=1S/C7H11N5O8P2/c8-7-11-5-4(6(13)12-7)10-3(1-9-5)2-19-22(17,18)20-21(14,15)16/h1-2H2,(H,17,18)(H2,14,15,16)(H4,8,9,11,12,13)

InChI Key

FCQGJGLSOWZZON-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
Organic pyrophosphate
Aminopyrimidine
Pyrimidone
Monoalkyl phosphate
Secondary aliphatic/aromatic amine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Ketimine
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Secondary amine
Primary amine
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Amine
Organic nitrogen compound
Imine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

pterin phosphate (CHEBI:15998 )
dihydropterin (CHEBI:15998 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	4.13 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-2.6	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.78	ChemAxon
pKa (Strongest Basic)	0.43	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	205.16 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	79.6 m³·mol⁻¹	ChemAxon
Polarizability	27.51 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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	splash10-002b-9721000000-7dd8d7f2621d27bc6a60	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0923000000-daae4676a03d5a81c9dc	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-0910000000-fbe617240fb10e7d245c	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0059-0900000000-8213899ab549e9639b96	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ufr-0509000000-6652a04120c6b6728e11	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-057i-9802000000-be3aa50bfc0d700c94b5	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-3071a16345027172ac91	2016-09-12	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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
nah	1		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C04807

BioCyc ID

DIHYDROPTERIN-CH2OH-PP

BiGG ID

Not Available

Wikipedia Link

2-Amino-4-hydroxy-6-pyrophosphoryl-methylpteridine

METLIN ID

Not Available

PubChem Compound

666

PDB ID

Not Available

ChEBI ID

15998

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for H2-6-Hydroxymethylpterin (MMDBc0009165)

MOL for #<Metabolite:0x00007f47067c4b48>

3D MOL for #<Metabolite:0x00007f47067c4b48>

3D SDF for #<Metabolite:0x00007f47067c4b48>

3D-SDF for #<Metabolite:0x00007f47067c4b48>

PDB for #<Metabolite:0x00007f47067c4b48>

3D PDB for #<Metabolite:0x00007f47067c4b48>

SMILES for #<Metabolite:0x00007f47067c4b48>

INCHI for #<Metabolite:0x00007f47067c4b48>

Structure for #<Metabolite:0x00007f47067c4b48>

3D Structure for #<Metabolite:0x00007f47067c4b48>