NP-MRD: Showing NP-Card for trans-zeatin riboside diphosphate (NP0339758)

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Record Information

Version

2.0

Created at

2024-09-11 23:24:30 UTC

Updated at

2024-09-11 23:24:30 UTC

NP-MRD ID

NP0339758

Secondary Accession Numbers

None

Natural Product Identification

Common Name

trans-zeatin riboside diphosphate

Description

Trans-zeatin riboside diphosphate belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety. Based on a literature review very few articles have been published on trans-zeatin riboside diphosphate.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05272301562D          

 33 35  0  0  0  0            999 V2000
    5.4223    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4223    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0098   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8348   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -2.3744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -3.1591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0728   -2.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1591   -3.4249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5084   -3.9098    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9933   -3.2424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0234   -4.5773    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.1758   -4.3947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0896   -5.2152    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0033   -6.0357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9101   -5.3015    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.2691   -5.1290    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7403   -1.2945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  2  0  0  0  0
  5  6  1  4  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 25 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 29 32  1  0  0  0  0
 22 33  1  0  0  0  0
 17 33  1  0  0  0  0
  8 13  1  0  0  0  0
M  CHG  3  27  -1  31  -1  32  -1
M  END


  Mrv2104 05272301562D          

 33 35  0  0  0  0            999 V2000
    5.4223    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7079    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4223    4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0098   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8348   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -2.3744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -3.1591    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7403   -2.1195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0728   -2.6044    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1591   -3.4249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5084   -3.9098    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9933   -3.2424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0234   -4.5773    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.1758   -4.3947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0896   -5.2152    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0033   -6.0357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9101   -5.3015    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.2691   -5.1290    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7403   -1.2945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  2  5  2  0  0  0  0
  5  6  1  4  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 25 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 29 32  1  0  0  0  0
 22 33  1  0  0  0  0
 17 33  1  0  0  0  0
  8 13  1  0  0  0  0
M  CHG  3  27  -1  31  -1  32  -1
M  END
> <DATABASE_ID>
NP0339758

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(CO)=CCNC1=NC=NC2=C1N=CN2C1OC(COP([O-])(=O)OP([O-])([O-])=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1/C15H23N5O11P2/c1-8(4-21)2-3-16-13-10-14(18-6-17-13)20(7-19-10)15-12(23)11(22)9(30-15)5-29-33(27,28)31-32(24,25)26/h2,6-7,9,11-12,15,21-23H,3-5H2,1H3,(H,27,28)(H,16,17,18)(H2,24,25,26)/p-3

> <INCHI_KEY>
MXFPFNSSZYNJGX-UHFFFAOYNA-K

> <FORMULA>
C15H20N5O11P2

> <MOLECULAR_WEIGHT>
508.298

> <EXACT_MASS>
508.06510122

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
44.74087660086353

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3,4-dihydroxy-5-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]-9H-purin-9-yl}oxolan-2-yl)methyl phosphonato]oxy}phosphonate

> <JCHEM_LOGP>
-4.326045094130645

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.22206414732252

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7674504994416762

> <JCHEM_PKA_STRONGEST_BASIC>
4.71428544095294

> <JCHEM_POLAR_SURFACE_AREA>
247.33

> <JCHEM_REFRACTIVITY>
107.96259999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(3,4-dihydroxy-5-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}oxolan-2-yl)methyl phosphonato]oxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0      10.122   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.788   6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.788   8.470   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      10.122   9.240   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.454   6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.454   4.620   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       6.121   3.850   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       7.454   1.540   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       7.454   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       6.121  -0.770   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       3.322   2.016   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       3.322  -0.476   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.752  -3.186   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       5.292  -3.186   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.846  -4.432   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       3.322  -5.897   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.382  -3.956   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.136  -4.862   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       0.297  -6.393   0.000  0.00  0.00           O+0
HETATM   25  P   UNK     0      -0.949  -7.298   0.000  0.00  0.00           P+0
HETATM   26  O   UNK     0      -1.854  -6.052   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -0.044  -8.544   0.000  0.00  0.00           O-1
HETATM   28  O   UNK     0      -2.195  -8.204   0.000  0.00  0.00           O+0
HETATM   29  P   UNK     0      -2.034  -9.735   0.000  0.00  0.00           P+0
HETATM   30  O   UNK     0      -1.873 -11.267   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -3.565  -9.896   0.000  0.00  0.00           O-1
HETATM   32  O   UNK     0      -0.502  -9.574   0.000  0.00  0.00           O-1
HETATM   33  O   UNK     0       1.382  -2.416   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14    8                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   12   17                                                  
CONECT   17   16   18   33                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   33                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27   28                                             
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   25   29                                                       
CONECT   29   28   30   31   32                                             
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   29                                                            
CONECT   33   22   17                                                       
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Value	Source
trans-Zeatin riboside diphosphoric acid	Generator

Chemical Formula

C₁₅H₂₀N₅O₁₁P₂

Average Mass

508.2980 Da

Monoisotopic Mass

508.06510 Da

IUPAC Name

{[(3,4-dihydroxy-5-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]-9H-purin-9-yl}oxolan-2-yl)methyl phosphonato]oxy}phosphonate

Traditional Name

[(3,4-dihydroxy-5-{6-[(4-hydroxy-3-methylbut-2-en-1-yl)amino]purin-9-yl}oxolan-2-yl)methyl phosphonato]oxyphosphonate

CAS Registry Number

Not Available

SMILES

CC(CO)=CCNC1=NC=NC2=C1N=CN2C1OC(COP([O-])(=O)OP([O-])([O-])=O)C(O)C1O

InChI Identifier

InChI=1/C15H23N5O11P2/c1-8(4-21)2-3-16-13-10-14(18-6-17-13)20(7-19-10)15-12(23)11(22)9(30-15)5-29-33(27,28)31-32(24,25)26/h2,6-7,9,11-12,15,21-23H,3-5H2,1H3,(H,27,28)(H,16,17,18)(H2,24,25,26)/p-3

InChI Key

MXFPFNSSZYNJGX-UHFFFAOYNA-K

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside diphosphates

Alternative Parents

Substituents

Purine ribonucleoside diphosphate
Purine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-alkylaminopurine
6-aminopurine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Secondary aliphatic/aromatic amine
Imidolactam
Alkyl phosphate
Monosaccharide
N-substituted imidazole
Pyrimidine
Organic phosphoric acid derivative
Phosphoric acid ester
Azole
Imidazole
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Azacycle
Organoheterocyclic compound
Secondary amine
Oxacycle
Organic oxide
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organic nitrogen compound
Primary alcohol
Organooxygen compound
Organopnictogen compound
Amine
Organonitrogen compound
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

a small molecule (CPD-4204 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-4.3	ChemAxon
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	4.71	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	247.33 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	107.96 m³·mol⁻¹	ChemAxon
Polarizability	44.74 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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

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Wikipedia Link

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METLIN ID

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PubChem Compound

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PDB ID

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ChEBI ID

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Good Scents ID

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References

General References

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Showing NP-Card for trans-zeatin riboside diphosphate (NP0339758)

MOL for NP0339758 (trans-zeatin riboside diphosphate)

3D MOL for NP0339758 (trans-zeatin riboside diphosphate)

3D SDF for NP0339758 (trans-zeatin riboside diphosphate)

3D-SDF for NP0339758 (trans-zeatin riboside diphosphate)

PDB for NP0339758 (trans-zeatin riboside diphosphate)

3D PDB for NP0339758 (trans-zeatin riboside diphosphate)

SMILES for NP0339758 (trans-zeatin riboside diphosphate)

INCHI for NP0339758 (trans-zeatin riboside diphosphate)

Structure for NP0339758 (trans-zeatin riboside diphosphate)

3D Structure for NP0339758 (trans-zeatin riboside diphosphate)