MiMeDB: Showing metabocard for Dihydroneopterin monophosphate (MMDBc0031607)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:41:12 UTC

Update Date

2022-08-31 18:22:27 UTC

Metabolite ID

MMDBc0031607

Metabolite Identification

Common Name

Dihydroneopterin monophosphate

Description

Dihydroneopterin monophosphate is a member of the chemical class known as Biopterins and Derivatives. These are coenzymes containing a 2-amino-pteridine-4-one derivative. Dihdroneopterin monophosphate is an intermediate involved in tetrahydrofolate biosynthesis and salvage in E. coli. It is converted to 7,8-dihydroneopterin through an unknown phosphorylase enzyme.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08141218152D          

 24 25  0  0  0  0            999 V2000
   -0.7145   -1.2375    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
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    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
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    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
   -3.5724    2.8875    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.4454    3.1895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2704    1.7605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    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
  6  4  1  0  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
  4 15  1  6  0  0  0
  6 16  1  1  0  0  0
 17  8  1  0  0  0  0
 21  2  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  1  0  0  0  0
 22 20  2  0  0  0  0
 22 21  1  0  0  0  0
  4 23  1  6  0  0  0
  6 24  1  1  0  0  0
M  CHG  2  17  -1  18  -1
M  END
> <DATABASE_ID>
MMDBc0031607

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H14N5O7P/c10-9-13-7-5(8(17)14-9)12-3(1-11-7)6(16)4(15)2-21-22(18,19)20/h4,6,15-16H,1-2H2,(H2,18,19,20)(H4,10,11,13,14,17)/p-2/t4-,6+/m1/s1

> <INCHI_KEY>
PLSQMGZYOGSOCE-XINAWCOVSA-L

> <FORMULA>
C9H12N5O7P

> <MOLECULAR_WEIGHT>
333.1946

> <EXACT_MASS>
333.047434275

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
27.098911407390023

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[(1S,2R)-3-(hydrogen phosphonatooxy)-1,2-dihydroxypropyl]-2-imino-1,2,7,8-tetrahydropteridin-4-olate

> <ALOGPS_LOGP>
-1.69

> <JCHEM_LOGP>
-5.7960995025194295

> <ALOGPS_LOGS>
-2.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
1.4973239366687876

> <JCHEM_PKA_STRONGEST_ACIDIC>
-13.061769204955379

> <JCHEM_PKA_STRONGEST_BASIC>
15.08231058413629

> <JCHEM_POLAR_SURFACE_AREA>
205.73999999999998

> <JCHEM_REFRACTIVITY>
100.97299999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.29e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-[(1S,2R)-3-(hydrogen phosphonatooxy)-1,2-dihydroxypropyl]-2-imino-7,8-dihydro-1H-pteridin-4-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3   11                                                       
CONECT    2    4   21                                                       
CONECT    3    1    6   12                                                  
CONECT    4    2    6   15   23                                             
CONECT    5    7    8   12                                                  
CONECT    6    3    4   16   24                                             
CONECT    7    5   11   13                                                  
CONECT    8    5   14   17                                                  
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    4                                                            
CONECT   16    6                                                            
CONECT   17    8                                                            
CONECT   18   22                                                            
CONECT   19   22                                                            
CONECT   20   22                                                            
CONECT   21    2   22                                                       
CONECT   22   18   19   20   21                                             
CONECT   23    4                                                            
CONECT   24    6                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

Synonyms

Value	Source
7,8-Dihydroneopterin 3'-phosphoric acid	Generator
7,8-Dihydroneopterin 3'-phosphate	ChEBI
Dihydroneopterin monophosphoric acid	Generator

Molecular Formula

C₉H₁₂N₅O₇P

Average Mass

333.1946

Monoisotopic Mass

333.047434275

IUPAC Name

6-[(1S,2R)-3-(hydrogen phosphonatooxy)-1,2-dihydroxypropyl]-2-imino-1,2,7,8-tetrahydropteridin-4-olate

Traditional Name

6-[(1S,2R)-3-(hydrogen phosphonatooxy)-1,2-dihydroxypropyl]-2-imino-7,8-dihydro-1H-pteridin-4-olate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H14N5O7P/c10-9-13-7-5(8(17)14-9)12-3(1-11-7)6(16)4(15)2-21-22(18,19)20/h4,6,15-16H,1-2H2,(H2,18,19,20)(H4,10,11,13,14,17)/p-2/t4-,6+/m1/s1

InChI Key

PLSQMGZYOGSOCE-XINAWCOVSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as biopterins and derivatives. These are coenzymes containing a 2-amino-pteridine-4-one derivative. They are mainly synthesized in several parts of the body, including the pineal gland.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pteridines and derivatives

Sub Class

Pterins and derivatives

Direct Parent

Biopterins and derivatives

Alternative Parents

Substituents

Biopterin
Aminopyrimidine
Pyrimidone
Secondary aliphatic/aromatic amine
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
1,2-diol
Ketimine
Secondary alcohol
Azacycle
Secondary amine
Hydrocarbon derivative
Primary amine
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Alcohol
Imine
Organic oxygen compound
Organic nitrogen compound
Amine
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:58762 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.29 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-5.8	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	-13	ChemAxon
pKa (Strongest Basic)	15.08	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	205.74 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	100.97 m³·mol⁻¹	ChemAxon
Polarizability	27.1 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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-1009000000-35334543f830e03972d5	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0032-5119000000-8a1311553ff5e2a2a732	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01qd-9741000000-f826bc486977b4d9a121	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-1009000000-a036e9146b5363f6c194	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001i-9002000000-60f9db77669111782949	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-003s-9000000000-116e1778470f092edb9c	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0008034	Dihydroneopterin triphosphate	Dihydroneopterin monophosphate	Not Available		VMH	30371894
MMDBr0008476	Dihydroneopterin monophosphate	Dihydroneopterin	Not Available		VMH	30371894

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	76	Pig ; Human feces; Human sputum; Human ; Human feces; pleural fluid plaque; bal; Human stool	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	19	Human feces; Human	Metabolic reconstruction
Bacteria	Fusobacteria	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	4	Human feces; Human	Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	2

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 Feces	Detected but not Quantified									HMDB

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25245170

PDB ID

Not Available

ChEBI ID

58762

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 Dihydroneopterin monophosphate (MMDBc0031607)

MOL for #<Metabolite:0x00007feca60f61e0>

3D MOL for #<Metabolite:0x00007feca60f61e0>

3D SDF for #<Metabolite:0x00007feca60f61e0>

3D-SDF for #<Metabolite:0x00007feca60f61e0>

PDB for #<Metabolite:0x00007feca60f61e0>

3D PDB for #<Metabolite:0x00007feca60f61e0>

SMILES for #<Metabolite:0x00007feca60f61e0>

INCHI for #<Metabolite:0x00007feca60f61e0>

Structure for #<Metabolite:0x00007feca60f61e0>

3D Structure for #<Metabolite:0x00007feca60f61e0>