MiMeDB: Showing metabocard for dZMP (MMDBc0055963)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:11:54 UTC

Update Date

2025-10-07 16:09:28 UTC

Metabolite ID

MMDBc0055963

Metabolite Identification

Common Name

dZMP

Description

dZMP is a nucleoside monophosphate that belongs to the class of nucleotides. Its chemical structure includes a ribose sugar, a phosphate group, and a nitrogenous base, which allows it to participate in various biochemical pathways. dZMP is involved in the incorporation processes of DNA polymerases, specifically the Klenow fragment and RB69 polymerase, which can incorporate dZMP opposite to 8-oxoG and 8-oxodGMP during DNA synthesis (PMID:38042029 ). Additionally, dZMP has been studied for its potential effects on gastrointestinal health, particularly in a model of functional constipation in Sprague-Dawley rats, where it was shown to enhance intestinal transit rates and regulate levels of gastrointestinal hormones and short-chain fatty acids (PMID:32846524 ). The administration of dZMP also resulted in significant alterations in the composition of intestinal microbiota, indicating its role in modulating gut flora (PMID:32846524 ). Furthermore, dZMP has been utilized in the synthesis of DNAzyme microparticles for environmental detection applications, showcasing its versatility beyond traditional nucleic acid functions (PMID:27169418 ). Overall, dZMP serves as a crucial component in both nucleic acid metabolism and potential therapeutic applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222112D          

 26 28  0  0  1  0            999 V2000
   -0.5546    2.5320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4916    3.4294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0396    3.1994    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8242    2.9445    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0396    1.8646    0.0000 C   0  0  2  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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -0.2549    0.0000 N   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
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846    3.9841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7403    5.2197    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.5879    5.4023    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -3.5577    4.0674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4054    4.2499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8242    2.1195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0728    4.7348    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6229    3.7828    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5593    2.5700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6229    1.2812    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  6  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  7  1  0  0  0  0
 11  8  1  0  0  0  0
 12 10  2  0  0  0  0
 13  3  2  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 14 10  1  0  0  0  0
 15  9  2  0  0  0  0
 15 10  1  0  0  0  0
 16  3  1  0  0  0  0
  6 16  1  6  0  0  0
 16  9  1  0  0  0  0
  4 17  1  1  0  0  0
 21  2  1  0  0  0  0
 22  5  1  0  0  0  0
 22  6  1  0  0  0  0
 23 18  1  0  0  0  0
 23 19  1  0  0  0  0
 23 20  2  0  0  0  0
 23 21  1  0  0  0  0
  4 24  1  6  0  0  0
  5 25  1  1  0  0  0
  6 26  1  1  0  0  0
M  CHG  2  18  -1  19  -1
M  END


  Mrv1652306172222112D          

 26 28  0  0  1  0            999 V2000
   -0.5546    2.5320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4916    3.4294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0396    3.1994    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8242    2.9445    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0396    1.8646    0.0000 C   0  0  2  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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -0.2549    0.0000 N   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
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846    3.9841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7403    5.2197    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.5879    5.4023    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -3.5577    4.0674    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4054    4.2499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8242    2.1195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0728    4.7348    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6229    3.7828    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5593    2.5700    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6229    1.2812    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  6  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  8  7  2  0  0  0  0
  9  7  1  0  0  0  0
 11  8  1  0  0  0  0
 12 10  2  0  0  0  0
 13  3  2  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 14 10  1  0  0  0  0
 15  9  2  0  0  0  0
 15 10  1  0  0  0  0
 16  3  1  0  0  0  0
  6 16  1  6  0  0  0
 16  9  1  0  0  0  0
  4 17  1  1  0  0  0
 21  2  1  0  0  0  0
 22  5  1  0  0  0  0
 22  6  1  0  0  0  0
 23 18  1  0  0  0  0
 23 19  1  0  0  0  0
 23 20  2  0  0  0  0
 23 21  1  0  0  0  0
  4 24  1  6  0  0  0
  5 25  1  1  0  0  0
  6 26  1  1  0  0  0
M  CHG  2  18  -1  19  -1
M  END
> <DATABASE_ID>
MMDBc0055963

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP([O-])([O-])=O)N1C=NC2=C(N)NC(=N)N=C12

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N6O6P/c11-8-7-9(15-10(12)14-8)16(3-13-7)6-1-4(17)5(22-6)2-21-23(18,19)20/h3-6,17H,1-2H2,(H2,18,19,20)(H4,11,12,14,15)/p-2/t4-,5+,6+/m0/s1

> <INCHI_KEY>
RZZBUMCFKOLHEH-KVQBGUIXSA-L

> <FORMULA>
C10H13N6O6P

> <MOLECULAR_WEIGHT>
344.225

> <EXACT_MASS>
344.06451632

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
29.570270192265102

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,5R)-5-(6-amino-2-imino-2,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphate

> <JCHEM_LOGP>
-2.906640552909525

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.258491963008123

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0615584236936213

> <JCHEM_PKA_STRONGEST_BASIC>
1.719330625759278

> <JCHEM_POLAR_SURFACE_AREA>
191.73999999999998

> <JCHEM_REFRACTIVITY>
93.28279999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,5R)-5-(6-amino-2-imino-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphate

> <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      -1.035   4.726   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.651   6.402   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.370   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.941   5.972   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.405   5.496   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.941   3.481   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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       4.001   2.310   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      -1.465  -0.476   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -1.465   2.016   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      -1.465   7.437   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -6.982   9.744   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0      -4.831  10.084   0.000  0.00  0.00           O-1
HETATM   20  O   UNK     0      -6.641   7.592   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -4.490   7.933   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -3.405   3.956   0.000  0.00  0.00           O+0
HETATM   23  P   UNK     0      -5.736   8.838   0.000  0.00  0.00           P+0
HETATM   24  H   UNK     0      -3.029   7.061   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      -4.777   4.797   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0      -3.029   2.392   0.000  0.00  0.00           H+0
CONECT    1    4    6                                                       
CONECT    2    5   21                                                       
CONECT    3   13   16                                                       
CONECT    4    1    5   17   24                                             
CONECT    5    2    4   22   25                                             
CONECT    6    1   16   22   26                                             
CONECT    7    8    9   13                                                  
CONECT    8    7   11   14                                                  
CONECT    9    7   15   16                                                  
CONECT   10   12   14   15                                                  
CONECT   11    8                                                            
CONECT   12   10                                                            
CONECT   13    3    7                                                       
CONECT   14    8   10                                                       
CONECT   15    9   10                                                       
CONECT   16    3    6    9                                                  
CONECT   17    4                                                            
CONECT   18   23                                                            
CONECT   19   23                                                            
CONECT   20   23                                                            
CONECT   21    2   23                                                       
CONECT   22    5    6                                                       
CONECT   23   18   19   20   21                                             
CONECT   24    4                                                            
CONECT   25    5                                                            
CONECT   26    6                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

Synonyms

Not Available

Molecular Formula

C₁₀H₁₃N₆O₆P

Average Mass

344.225

Monoisotopic Mass

344.06451632

IUPAC Name

[(2R,3S,5R)-5-(6-amino-2-imino-2,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphate

Traditional Name

[(2R,3S,5R)-5-(6-amino-2-imino-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphate

CAS Registry Number

Not Available

SMILES

[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP([O-])([O-])=O)N1C=NC2=C(N)NC(=N)N=C12

InChI Identifier

InChI=1S/C10H15N6O6P/c11-8-7-9(15-10(12)14-8)16(3-13-7)6-1-4(17)5(22-6)2-21-23(18,19)20/h3-6,17H,1-2H2,(H2,18,19,20)(H4,11,12,14,15)/p-2/t4-,5+,6+/m0/s1

InChI Key

RZZBUMCFKOLHEH-KVQBGUIXSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside monophosphates. These are purine nucleotides with monophosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine deoxyribonucleotides

Direct Parent

Purine 2'-deoxyribonucleoside monophosphates

Alternative Parents

Substituents

Purine 2'-deoxyribonucleoside monophosphate
6-aminopurine
Purine
Imidazopyrimidine
Aminopyrimidine
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
N-substituted imidazole
Heteroaromatic compound
Tetrahydrofuran
Imidazole
Azole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.9	ChemAxon
pKa (Strongest Acidic)	1.06	ChemAxon
pKa (Strongest Basic)	1.72	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	191.74 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	93.28 m³·mol⁻¹	ChemAxon
Polarizability	29.57 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

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
Bacteria	Proteobacteria	1	Human
Bacteria/Eubacteria	Proteobacteria	3	Human
Bacteria/Eubacteria	Cyanobacteria	8

Exposure Sources

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00003046

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

155920207

PDB ID

Not Available

ChEBI ID

172927

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 dZMP (MMDBc0055963)

MOL for #<Metabolite:0x0000561537b68238>

3D MOL for #<Metabolite:0x0000561537b68238>

3D SDF for #<Metabolite:0x0000561537b68238>

3D-SDF for #<Metabolite:0x0000561537b68238>

PDB for #<Metabolite:0x0000561537b68238>

3D PDB for #<Metabolite:0x0000561537b68238>

SMILES for #<Metabolite:0x0000561537b68238>

INCHI for #<Metabolite:0x0000561537b68238>

Structure for #<Metabolite:0x0000561537b68238>

3D Structure for #<Metabolite:0x0000561537b68238>