NP-MRD: Showing NP-Card for ADP-ribose 2'-phosphate (NP0136745)

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Record Information

Version

2.0

Created at

2022-05-12 15:22:26 UTC

Updated at

2022-05-12 15:22:26 UTC

NP-MRD ID

NP0136745

Secondary Accession Numbers

None

Natural Product Identification

Common Name

ADP-ribose 2'-phosphate

Description

ADP-ribose 2'-phosphate belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group. ADP-ribose 2'-phosphate is an intermediate metabolite in vitamin and cofactor metabolism, more specifically NAD metabolism. ADP-ribose 2'-phosphate is a strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304202019342D          

 40 43  0  0  0  0            999 V2000
    1.7855    2.3375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2145    2.3375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2145    3.1625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4840    2.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.5000    1.9250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9991    3.4174    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9991    2.0825    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5000    3.5750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5000    4.4000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7612    0.7481    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    3.5062   -0.0365    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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  9  5  2  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304202019342D          

 40 43  0  0  0  0            999 V2000
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 32 33  1  6  0  0  0
 34 35  1  6  0  0  0
 36 39  1  0  0  0  0
 39 37  2  0  0  0  0
 39 38  1  0  0  0  0
 39 40  1  0  0  0  0
 27 26  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0136745

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)O[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)[C@@H](O)[C@H]1OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H24N5O17P3/c16-12-7-13(18-3-17-12)20(4-19-7)14-11(35-38(25,26)27)9(23)6(33-14)2-32-39(28,29)37-40(30,31)36-15-10(24)8(22)5(1-21)34-15/h3-6,8-11,14-15,21-24H,1-2H2,(H,28,29)(H,30,31)(H2,16,17,18)(H2,25,26,27)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1

> <INCHI_KEY>
OCOLIMYIUOUURJ-ZQSHOCFMSA-N

> <FORMULA>
C15H24N5O17P3

> <MOLECULAR_WEIGHT>
639.2956

> <EXACT_MASS>
639.038003903

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
51.33523479899604

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3R,4R,5R)-2-(6-amino-9H-purin-9-yl)-5-[({[({[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-4-hydroxyoxolan-3-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.43

> <JCHEM_LOGP>
-6.603915203932898

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.7655534743465608

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.646819020023043

> <JCHEM_PKA_STRONGEST_BASIC>
3.9861969638247627

> <JCHEM_POLAR_SURFACE_AREA>
338.05

> <JCHEM_REFRACTIVITY>
121.9962

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.97e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
adp-ribose 2'-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0       3.333   4.363   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.000   4.363   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.000   5.903   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.370   5.133   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.333   5.903   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       4.667   3.593   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       7.465   6.379   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       7.465   3.887   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       4.667   6.673   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       4.667   8.213   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       7.021   1.396   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.775   2.302   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.545  -0.068   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.005  -0.068   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.235  -1.402   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       4.529   1.396   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.295   2.196   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.107   1.715   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -0.973   1.715   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.567   3.255   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0       0.567   1.715   0.000  0.00  0.00           P+0
HETATM   22  O   UNK     0       0.567   0.175   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -2.513   3.255   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0      -2.513   1.715   0.000  0.00  0.00           P+0
HETATM   25  O   UNK     0      -2.513   0.175   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -4.053   1.715   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -5.387   0.945   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -6.633   1.851   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -7.879   0.945   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -9.213   1.715   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0     -10.546   0.945   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -5.863  -0.519   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -5.093  -1.853   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -7.403  -0.519   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -8.173  -1.853   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       7.315  -1.402   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       5.775  -2.942   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       8.855  -2.942   0.000  0.00  0.00           O+0
HETATM   39  P   UNK     0       7.315  -2.942   0.000  0.00  0.00           P+0
HETATM   40  O   UNK     0       7.315  -4.482   0.000  0.00  0.00           O+0
CONECT    1    5    6                                                       
CONECT    2    6    8    3                                                  
CONECT    3    9    2    7                                                  
CONECT    4    7    8                                                       
CONECT    5    9    1                                                       
CONECT    6    1    2                                                       
CONECT    7    3    4                                                       
CONECT    8    2    4   11                                                  
CONECT    9    5    3   10                                                  
CONECT   10    9                                                            
CONECT   11   12   13    8                                                  
CONECT   12   16   11                                                       
CONECT   13   14   11   36                                                  
CONECT   14   16   13   15                                                  
CONECT   15   14                                                            
CONECT   16   12   14   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   21                                                       
CONECT   19   21   24                                                       
CONECT   20   21                                                            
CONECT   21   18   19   20   22                                             
CONECT   22   21                                                            
CONECT   23   24                                                            
CONECT   24   19   26   23   25                                             
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   32   28   26                                                  
CONECT   28   27   29                                                       
CONECT   29   28   34   30                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   27   34   33                                                  
CONECT   33   32                                                            
CONECT   34   29   32   35                                                  
CONECT   35   34                                                            
CONECT   36   13   39                                                       
CONECT   37   39                                                            
CONECT   38   39                                                            
CONECT   39   36   37   38   40                                             
CONECT   40   39                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   86    0
END

View in JSmol

Synonyms

Value	Source
ADP-Ribose 2'-phosphoric acid	Generator
2'-Phosphoadenosine 5'-[3-(D-ribofuranosyl) dihydrogen diphosphate]	HMDB
ADP-D-Ribose 2'-phosphate	HMDB
ADPribose 2'-phosphate	HMDB
{[(2R,3R,4R,5R)-2-(6-amino-9H-purin-9-yl)-5-[({[({[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-4-hydroxyoxolan-3-yl]oxy}phosphonate	HMDB
Adenosine 2'-phosphate 5'-diphosphate ribose	HMDB
Adenosine 2’-phosphate 5’-diphosphate ribose	HMDB

Chemical Formula

C₁₅H₂₄N₅O₁₇P₃

Average Mass

639.2956 Da

Monoisotopic Mass

639.03800 Da

IUPAC Name

{[(2R,3R,4R,5R)-2-(6-amino-9H-purin-9-yl)-5-[({[({[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-4-hydroxyoxolan-3-yl]oxy}phosphonic acid

Traditional Name

adp-ribose 2'-phosphate

CAS Registry Number

Not Available

SMILES

NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)O[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)[C@@H](O)[C@H]1OP(O)(O)=O

InChI Identifier

InChI=1S/C15H24N5O17P3/c16-12-7-13(18-3-17-12)20(4-19-7)14-11(35-38(25,26)27)9(23)6(33-14)2-32-39(28,29)37-40(30,31)36-15-10(24)8(22)5(1-21)34-15/h3-6,8-11,14-15,21-24H,1-2H2,(H,28,29)(H,30,31)(H2,16,17,18)(H2,25,26,27)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1

InChI Key

OCOLIMYIUOUURJ-ZQSHOCFMSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine nucleotide sugars

Direct Parent

Purine nucleotide sugars

Alternative Parents

Substituents

Purine nucleotide sugar
Purine ribonucleoside 2',5'-bisphosphate
Purine ribonucleoside bisphosphate
Purine ribonucleoside diphosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-aminopurine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
Pyrimidine
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Imidolactam
Alkyl phosphate
Tetrahydrofuran
Azole
Heteroaromatic compound
Imidazole
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Amine
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Organopnictogen compound
Primary alcohol
Primary amine
Organonitrogen compound
Organooxygen compound
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	-1.4	ALOGPS
logP	-6.6	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	0.65	ChemAxon
pKa (Strongest Basic)	3.99	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	338.05 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	122 m³·mol⁻¹	ChemAxon
Polarizability	51.34 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon