MiMeDB: Showing metabocard for 7,8-dihydroneopterin 2',3'-cyclic phosphate (MMDBc0055630)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:00:51 UTC

Update Date

2022-08-12 20:09:26 UTC

Metabolite ID

MMDBc0055630

Metabolite Identification

Common Name

7,8-dihydroneopterin 2',3'-cyclic phosphate

Description

7,8-dihydro-D-neopterin 2',3'-cyclic phosphate(1-) 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. Based on a literature review very few articles have been published on 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate(1-).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222002D          

 23 25  0  0  1  0            999 V2000
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2296   -1.2330    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
   -2.1434   -0.4125    0.0000 C   0  0  2  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 C   0  0  1  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
    1.4289    0.0000    0.0000 C   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
    2.8579   -1.6500    0.0000 N   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
    0.0000    0.0000    0.0000 N   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
    2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -4.1166   -1.1750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0012   -0.0769    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0366   -1.4045    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8971   -0.0769    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4491   -0.6900    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1866    0.4114    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  3  1  0  0  0  0
  4  6  1  1  0  0  0
  7  5  2  0  0  0  0
  8  5  1  0  0  0  0
 10  9  2  0  0  0  0
 11  1  1  0  0  0  0
 11  7  1  0  0  0  0
 12  3  2  0  0  0  0
 12  5  1  0  0  0  0
 13  7  1  0  0  0  0
 13  9  1  0  0  0  0
 14  8  2  0  0  0  0
 14  9  1  0  0  0  0
  6 15  1  6  0  0  0
 16  8  1  0  0  0  0
 19  2  1  0  0  0  0
 20  4  1  0  0  0  0
 21 17  1  0  0  0  0
 21 18  2  0  0  0  0
 21 19  1  0  0  0  0
 21 20  1  0  0  0  0
  4 22  1  6  0  0  0
  6 23  1  6  0  0  0
M  CHG  1  16  -1
M  END
> <DATABASE_ID>
MMDBc0055630

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(C1=NC2=C(NC1)NC(=N)N=C2[O-])[C@@]1([H])COP(O)(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N5O6P/c10-9-13-7-5(8(16)14-9)12-3(1-11-7)6(15)4-2-19-21(17,18)20-4/h4,6,15H,1-2H2,(H,17,18)(H4,10,11,13,14,16)/p-1/t4-,6+/m1/s1

> <INCHI_KEY>
QXDMVWOCXHMTPE-XINAWCOVSA-M

> <FORMULA>
C9H11N5O6P

> <MOLECULAR_WEIGHT>
316.19

> <EXACT_MASS>
316.045243672

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
25.948380145741964

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[(S)-hydroxy[(4R)-2-hydroxy-2-oxo-1,3,2lambda5-dioxaphospholan-4-yl]methyl]-2-imino-1,2,7,8-tetrahydropteridin-4-olate

> <JCHEM_LOGP>
-2.275548587265739

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
5.364810328595277

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.056796473982647

> <JCHEM_PKA_STRONGEST_BASIC>
1.4417938428435098

> <JCHEM_POLAR_SURFACE_AREA>
171.67999999999998

> <JCHEM_REFRACTIVITY>
98.31569999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-[(S)-hydroxy[(4R)-2-hydroxy-2-oxo-1,3,2lambda5-dioxaphospholan-4-yl]methyl]-2-imino-7,8-dihydro-1H-pteridin-4-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.162  -2.302   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.001  -0.770   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      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       5.335  -3.080   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000  -3.080   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       2.667  -3.080   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0      -7.684  -2.193   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -7.469  -0.144   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -5.668  -2.622   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -5.408  -0.144   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0      -6.438  -1.288   0.000  0.00  0.00           P+0
HETATM   22  H   UNK     0      -4.082   0.768   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0      -2.667  -1.540   0.000  0.00  0.00           H+0
CONECT    1    3   11                                                       
CONECT    2    4   19                                                       
CONECT    3    1    6   12                                                  
CONECT    4    2    6   20   22                                             
CONECT    5    7    8   12                                                  
CONECT    6    3    4   15   23                                             
CONECT    7    5   11   13                                                  
CONECT    8    5   14   16                                                  
CONECT    9   10   13   14                                                  
CONECT   10    9                                                            
CONECT   11    1    7                                                       
CONECT   12    3    5                                                       
CONECT   13    7    9                                                       
CONECT   14    8    9                                                       
CONECT   15    6                                                            
CONECT   16    8                                                            
CONECT   17   21                                                            
CONECT   18   21                                                            
CONECT   19    2   21                                                       
CONECT   20    4   21                                                       
CONECT   21   17   18   19   20                                             
CONECT   22    4                                                            
CONECT   23    6                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

Synonyms

Value	Source
(4R)-4-[(S)-(2-Amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)(hydroxy)methyl]-2-oxo-1,3,2lambda(5)-dioxaphospholan-2-olate	ChEBI
7,8-Dihydroneopterin 2',3'-cyclic phosphate	ChEBI
(4R)-4-[(S)-(2-Amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)(hydroxy)methyl]-2-oxo-1,3,2lambda(5)-dioxaphospholan-2-olic acid	Generator
7,8-Dihydroneopterin 2',3'-cyclic phosphoric acid	Generator
7,8-Dihydro-D-neopterin 2',3'-cyclic phosphoric acid(1-)	Generator

Molecular Formula

C₉H₁₁N₅O₆P

Average Mass

316.19

Monoisotopic Mass

316.045243672

IUPAC Name

6-[(S)-hydroxy[(4R)-2-hydroxy-2-oxo-1,3,2lambda5-dioxaphospholan-4-yl]methyl]-2-imino-1,2,7,8-tetrahydropteridin-4-olate

Traditional Name

6-[(S)-hydroxy[(4R)-2-hydroxy-2-oxo-1,3,2lambda5-dioxaphospholan-4-yl]methyl]-2-imino-7,8-dihydro-1H-pteridin-4-olate

CAS Registry Number

Not Available

SMILES

[H][C@](O)(C1=NC2=C(NC1)NC(=N)N=C2[O-])[C@@]1([H])COP(O)(=O)O1

InChI Identifier

InChI=1S/C9H12N5O6P/c10-9-13-7-5(8(16)14-9)12-3(1-11-7)6(15)4-2-19-21(17,18)20-4/h4,6,15H,1-2H2,(H,17,18)(H4,10,11,13,14,16)/p-1/t4-,6+/m1/s1

InChI Key

QXDMVWOCXHMTPE-XINAWCOVSA-M

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
Aminopyrimidine
Pyrimidone
Secondary aliphatic/aromatic amine
Organic phosphoric acid derivative
Pyrimidine
1,3_dioxaphospholane
Heteroaromatic compound
Vinylogous amide
Ketimine
Secondary alcohol
Azacycle
Oxacycle
Secondary amine
Amine
Hydrocarbon derivative
Organic oxide
Primary amine
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Alcohol
Imine
Organic oxygen compound
Organic nitrogen compound
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:58854 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.3	ChemAxon
pKa (Strongest Acidic)	2.06	ChemAxon
pKa (Strongest Basic)	1.44	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	171.68 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	98.32 m³·mol⁻¹	ChemAxon
Polarizability	25.95 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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

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
Archaea/Archaea	Crenarchaeota	1
Archaea/Archaea	Euryarchaeota	33
Archaea/Archaea	Korarchaeota	1
Archaea	Euryarchaeota	2

Exposure Sources

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

26331402

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44123427

PDB ID

Not Available

ChEBI ID

58854

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 7,8-dihydroneopterin 2',3'-cyclic phosphate (MMDBc0055630)

MOL for #<Metabolite:0x00007fdb44008e40>

3D MOL for #<Metabolite:0x00007fdb44008e40>

3D SDF for #<Metabolite:0x00007fdb44008e40>

3D-SDF for #<Metabolite:0x00007fdb44008e40>

PDB for #<Metabolite:0x00007fdb44008e40>

3D PDB for #<Metabolite:0x00007fdb44008e40>

SMILES for #<Metabolite:0x00007fdb44008e40>

INCHI for #<Metabolite:0x00007fdb44008e40>

Structure for #<Metabolite:0x00007fdb44008e40>

3D Structure for #<Metabolite:0x00007fdb44008e40>