MiMeDB: Showing metabocard for dZDP (MMDBc0055962)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:11:53 UTC

Update Date

2025-10-07 16:09:28 UTC

Metabolite ID

MMDBc0055962

Metabolite Identification

Common Name

dZDP

Description

dZDP is a computational basis set used in quantum chemistry, particularly in density functional theory (DFT) calculations. Its chemical structure is characterized by a specific arrangement of basis functions that facilitate the accurate modeling of electron interactions in complex molecular systems. dZDP is employed in various computational frameworks, such as the SIESTA software, to explore interactions between small molecules, cations, and nucleic acids, including duplex DNA and G-quadruplexes. For instance, studies have utilized the LMKLL/DZDP level of calculation to incorporate van der Waals forces in simulations involving biological systems with approximately 1000 atoms (PMID:36260061 ). Furthermore, the LMKLL/DZDP method has been shown to provide precise geometries and energetics for diverse molecular configurations, including those involving intercalating agents in DNA and metal-G-tetrads with varying alkaline metal sizes (PMID:35362496 ). This highlights dZDP's role in enhancing the accuracy of theoretical predictions in biochemical pathways and molecular interactions, making it a valuable tool in computational biochemistry (PMID:36973447 ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222112D          

 30 32  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
   -6.0875    3.3926    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -5.6694    4.4818    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -4.9983    2.9745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4278    4.2462    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -4.3977    2.9113    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2453    3.0939    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
   -4.5802    4.0637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3338    3.7282    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9127    3.5788    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
 23  2  1  0  0  0  0
 24  5  1  0  0  0  0
 24  6  1  0  0  0  0
 26 18  1  0  0  0  0
 26 19  1  0  0  0  0
 26 20  2  0  0  0  0
 26 25  1  0  0  0  0
 27 21  1  0  0  0  0
 27 22  2  0  0  0  0
 27 23  1  0  0  0  0
 27 25  1  0  0  0  0
  4 28  1  6  0  0  0
  5 29  1  1  0  0  0
  6 30  1  1  0  0  0
M  CHG  3  18  -1  19  -1  21  -1
M  END


  Mrv1652306172222112D          

 30 32  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
   -6.0875    3.3926    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -5.6694    4.4818    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -4.9983    2.9745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4278    4.2462    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -4.3977    2.9113    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2453    3.0939    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
   -4.5802    4.0637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3338    3.7282    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9127    3.5788    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
 23  2  1  0  0  0  0
 24  5  1  0  0  0  0
 24  6  1  0  0  0  0
 26 18  1  0  0  0  0
 26 19  1  0  0  0  0
 26 20  2  0  0  0  0
 26 25  1  0  0  0  0
 27 21  1  0  0  0  0
 27 22  2  0  0  0  0
 27 23  1  0  0  0  0
 27 25  1  0  0  0  0
  4 28  1  6  0  0  0
  5 29  1  1  0  0  0
  6 30  1  1  0  0  0
M  CHG  3  18  -1  19  -1  21  -1
M  END
> <DATABASE_ID>
MMDBc0055962

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H16N6O9P2/c11-8-7-9(15-10(12)14-8)16(3-13-7)6-1-4(17)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,17H,1-2H2,(H,21,22)(H2,18,19,20)(H4,11,12,14,15)/p-3/t4-,5+,6+/m0/s1

> <INCHI_KEY>
VYJMSGDLIGSRJI-KVQBGUIXSA-K

> <FORMULA>
C10H13N6O9P2

> <MOLECULAR_WEIGHT>
423.196

> <EXACT_MASS>
423.023570758

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
33.86821168324783

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-3

> <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 phosphono}oxy)phosphonate

> <JCHEM_LOGP>
-3.2226141176658083

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.2197500107264267

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9657744578433807

> <JCHEM_PKA_STRONGEST_BASIC>
1.3445963492437734

> <JCHEM_POLAR_SURFACE_AREA>
241.09999999999997

> <JCHEM_REFRACTIVITY>
103.03399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <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 phosphono}oxyphosphonate

> <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     -11.363   6.333   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0     -10.583   8.366   0.000  0.00  0.00           O-1
HETATM   20  O   UNK     0      -9.330   5.552   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -6.399   7.926   0.000  0.00  0.00           O-1
HETATM   22  O   UNK     0      -8.209   5.435   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -6.058   5.775   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -3.405   3.956   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -8.550   7.586   0.000  0.00  0.00           O+0
HETATM   26  P   UNK     0      -9.957   6.959   0.000  0.00  0.00           P+0
HETATM   27  P   UNK     0      -7.304   6.680   0.000  0.00  0.00           P+0
HETATM   28  H   UNK     0      -3.029   7.061   0.000  0.00  0.00           H+0
HETATM   29  H   UNK     0      -4.777   4.797   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0      -3.029   2.392   0.000  0.00  0.00           H+0
CONECT    1    4    6                                                       
CONECT    2    5   23                                                       
CONECT    3   13   16                                                       
CONECT    4    1    5   17   28                                             
CONECT    5    2    4   24   29                                             
CONECT    6    1   16   24   30                                             
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   26                                                            
CONECT   19   26                                                            
CONECT   20   26                                                            
CONECT   21   27                                                            
CONECT   22   27                                                            
CONECT   23    2   27                                                       
CONECT   24    5    6                                                       
CONECT   25   26   27                                                       
CONECT   26   18   19   20   25                                             
CONECT   27   21   22   23   25                                             
CONECT   28    4                                                            
CONECT   29    5                                                            
CONECT   30    6                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   64    0
END

Synonyms

Not Available

Molecular Formula

C₁₀H₁₃N₆O₉P₂

Average Mass

423.196

Monoisotopic Mass

423.023570758

IUPAC Name

({[(2R,3S,5R)-5-(6-amino-2-imino-2,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphono}oxy)phosphonate

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C10H16N6O9P2/c11-8-7-9(15-10(12)14-8)16(3-13-7)6-1-4(17)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,17H,1-2H2,(H,21,22)(H2,18,19,20)(H4,11,12,14,15)/p-3/t4-,5+,6+/m0/s1

InChI Key

VYJMSGDLIGSRJI-KVQBGUIXSA-K

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate 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 diphosphates

Alternative Parents

Substituents

Purine 2'-deoxyribonucleoside diphosphate
Organic pyrophosphate
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	-3.2	ChemAxon
pKa (Strongest Acidic)	1.97	ChemAxon
pKa (Strongest Basic)	1.34	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	241.1 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	103.03 m³·mol⁻¹	ChemAxon
Polarizability	33.87 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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	Microbial Links
Bacteria/Eubacteria	Cyanobacteria	10
Bacteria/Eubacteria	Proteobacteria	11	Human ; Human feces

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

C00023813

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

155920208

PDB ID

Not Available

ChEBI ID

172929

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 dZDP (MMDBc0055962)

MOL for #<Metabolite:0x0000561537e09258>

3D MOL for #<Metabolite:0x0000561537e09258>

3D SDF for #<Metabolite:0x0000561537e09258>

3D-SDF for #<Metabolite:0x0000561537e09258>

PDB for #<Metabolite:0x0000561537e09258>

3D PDB for #<Metabolite:0x0000561537e09258>

SMILES for #<Metabolite:0x0000561537e09258>

INCHI for #<Metabolite:0x0000561537e09258>

Structure for #<Metabolite:0x0000561537e09258>

3D Structure for #<Metabolite:0x0000561537e09258>