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Showing NP-Card for ADP (NP0334068)

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Record Information
Version2.0
Created at2024-09-09 22:01:10 UTC
Updated at2024-09-09 22:01:11 UTC
NP-MRD IDNP0334068
Secondary Accession NumbersNone
Natural Product Identification
Common NameADP
DescriptionAdenosine diphosphate, abbreviated ADP, is a nucleotide. It is an ester of pyrophosphoric acid with the nucleotide adenine. ADP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase adenine. ADP is the product of ATP dephosphorylation by ATPases. ADP is converted back to ATP by ATP synthases. [HMDB]. ADP is found in many foods, some of which are american cranberry, peanut, abalone, and strawberry.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0334068 (ADP)


  Mrv2104 05252300332D          

 27 29  0  0  0  0            999 V2000
   -0.5683    4.5399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992    4.0549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    4.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687    3.6424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    5.0945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937    3.6424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1642    4.5030    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7461    5.5923    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0749    4.0849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5045    5.3567    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4743    4.0218    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3220    4.2043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992    3.2299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6568    5.1742    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4105    4.8386    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9894    4.6892    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  1 23  1  0  0  0  0
  2 12  2  0  0  0  0
  2 13  1  0  0  0  0
  3 14  2  0  0  0  0
  3 15  1  0  0  0  0
  4  6  1  0  0  0  0
  4 24  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  5 14  1  0  0  0  0
  6  7  1  0  0  0  0
  6 16  1  0  0  0  0
  7 10  1  0  0  0  0
  7 17  1  0  0  0  0
  8 11  1  0  0  0  0
  8 12  1  0  0  0  0
  9 13  2  0  0  0  0
  9 15  1  0  0  0  0
 10 15  1  0  0  0  0
 10 24  1  0  0  0  0
 18 26  1  0  0  0  0
 19 26  1  0  0  0  0
 20 26  2  0  0  0  0
 21 27  1  0  0  0  0
 22 27  2  0  0  0  0
 23 27  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
M  END
Download

3D MOL for NP0334068 (ADP)

Download
3D SDF for NP0334068 (ADP)

  Mrv2104 05252300332D          

 27 29  0  0  0  0            999 V2000
   -0.5683    4.5399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992    4.0549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    4.3099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687    3.6424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    2.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    5.0945    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937    3.6424    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1642    4.5030    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7461    5.5923    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0749    4.0849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5045    5.3567    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4743    4.0218    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3220    4.2043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992    3.2299    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6568    5.1742    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4105    4.8386    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9894    4.6892    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  1 23  1  0  0  0  0
  2 12  2  0  0  0  0
  2 13  1  0  0  0  0
  3 14  2  0  0  0  0
  3 15  1  0  0  0  0
  4  6  1  0  0  0  0
  4 24  1  0  0  0  0
  5  8  2  0  0  0  0
  5  9  1  0  0  0  0
  5 14  1  0  0  0  0
  6  7  1  0  0  0  0
  6 16  1  0  0  0  0
  7 10  1  0  0  0  0
  7 17  1  0  0  0  0
  8 11  1  0  0  0  0
  8 12  1  0  0  0  0
  9 13  2  0  0  0  0
  9 15  1  0  0  0  0
 10 15  1  0  0  0  0
 10 24  1  0  0  0  0
 18 26  1  0  0  0  0
 19 26  1  0  0  0  0
 20 26  2  0  0  0  0
 21 27  1  0  0  0  0
 22 27  2  0  0  0  0
 23 27  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334068

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=C2N=CN(C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O)C2=NC=N1

> <INCHI_IDENTIFIER>
InChI=1/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)

> <INCHI_KEY>
XTWYTFMLZFPYCI-UHFFFAOYNA-N

> <FORMULA>
C10H15N5O10P2

> <MOLECULAR_WEIGHT>
427.203

> <EXACT_MASS>
427.029415699

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
34.82329856249039

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <JCHEM_LOGP>
-4.826808719758876

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.222647778622181

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.769425192137052

> <JCHEM_PKA_STRONGEST_BASIC>
4.9281186654632245

> <JCHEM_POLAR_SURFACE_AREA>
232.59999999999994

> <JCHEM_REFRACTIVITY>
84.94139999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
adenosine diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0334068 (ADP)
Download
PDB for NP0334068 (ADP)
HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0      -1.061   8.474   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.185   7.569   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.650   8.045   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.555   6.799   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.650   5.553   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       4.924  -0.237   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       6.258   2.073   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       4.924   4.383   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       2.126   9.510   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.095   6.799   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -7.773   8.406   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -6.993  10.439   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -5.740   7.625   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.808   9.999   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -4.619   7.507   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -2.468   7.848   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.185   6.029   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -4.959   9.658   0.000  0.00  0.00           O+0
HETATM   26  P   UNK     0      -6.366   9.032   0.000  0.00  0.00           P+0
HETATM   27  P   UNK     0      -3.714   8.753   0.000  0.00  0.00           P+0
CONECT    1    4   23                                                       
CONECT    2   12   13                                                       
CONECT    3   14   15                                                       
CONECT    4    1    6   24                                                  
CONECT    5    8    9   14                                                  
CONECT    6    4    7   16                                                  
CONECT    7    6   10   17                                                  
CONECT    8    5   11   12                                                  
CONECT    9    5   13   15                                                  
CONECT   10    7   15   24                                                  
CONECT   11    8                                                            
CONECT   12    2    8                                                       
CONECT   13    2    9                                                       
CONECT   14    3    5                                                       
CONECT   15    3    9   10                                                  
CONECT   16    6                                                            
CONECT   17    7                                                            
CONECT   18   26                                                            
CONECT   19   26                                                            
CONECT   20   26                                                            
CONECT   21   27                                                            
CONECT   22   27                                                            
CONECT   23    1   27                                                       
CONECT   24    4   10                                                       
CONECT   25   26   27                                                       
CONECT   26   18   19   20   25                                             
CONECT   27   21   22   23   25                                             
MASTER        0    0    0    0    0    0    0    0   27    0   58    0
END

Download
3D PDB for NP0334068 (ADP)
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SMILES for NP0334068 (ADP)
NC1=C2N=CN(C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O)C2=NC=N1
Download
INCHI for NP0334068 (ADP)
InChI=1/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)
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View in JSmol
SynonymsNot Available
Chemical FormulaC10H15N5O10P2
Average Mass427.2030 Da
Monoisotopic Mass427.02942 Da
IUPAC Name[({[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional Nameadenosine diphosphate
CAS Registry NumberNot Available
SMILES
NC1=C2N=CN(C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O)C2=NC=N1
InChI Identifier
InChI=1/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)
InChI KeyXTWYTFMLZFPYCI-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis 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.
KingdomOrganic compounds  
Super ClassNucleosides, nucleotides, and analogues  
ClassPurine nucleotides  
Sub ClassPurine ribonucleotides  
Direct ParentPurine ribonucleoside diphosphates  
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
    • 

  • Purine ribonucleoside monophosphate
    • 

  • Pentose phosphate
    • 

  • Pentose-5-phosphate
    • 

  • Glycosyl compound
    • 

  • N-glycosyl compound
    • 

  • 6-aminopurine
    • 

  • Monosaccharide phosphate
    • 

  • Organic pyrophosphate
    • 

  • Pentose monosaccharide
    • 

  • Imidazopyrimidine
    • 

  • Purine
    • 

  • Monoalkyl phosphate
    • 

  • Aminopyrimidine
    • 

  • Alkyl phosphate
    • 

  • Monosaccharide
    • 

  • N-substituted imidazole
    • 

  • Organic phosphoric acid derivative
    • 

  • Phosphoric acid ester
    • 

  • Imidolactam
    • 

  • Pyrimidine
    • 

  • Azole
    • 

  • Heteroaromatic compound
    • 

  • Imidazole
    • 

  • Tetrahydrofuran
    • 

  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • Azacycle
    • 

  • Oxacycle
    • 

  • Organoheterocyclic compound
    • 

  • Alcohol
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Primary amine
    • 

  • Amine
    • 

  • Hydrocarbon derivative
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-4.8ChemAxon
pKa (Strongest Acidic)1.77ChemAxon
pKa (Strongest Basic)4.93ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area232.6 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity84.94 m³·mol⁻¹ChemAxon
Polarizability34.82 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkADP  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Haziman ML, Ishaq MI, Qonit MAH, Lestari EG, Susilawati PN, Widarsih W, Syukur C, Herawati H, Arief R, Santosa B, Purba R, Andoyo R, Yursak Z, Tan SS, Musfal M, Mubarok S: Sorghum starch review: Structural properties, interactions with proteins and polyphenols, and modification of physicochemical properties. Food Chem. 2024 May 25;463(Pt 1):139810. doi: 10.1016/j.foodchem.2024.139810. [PubMed:39293183  ] 
  2. Soler-Garzon A, Mulube M, Kamfwa K, Lungu DM, Hamabwe S, Roy J, Salegua V, Fourie D, Porch TG, McClean PE, Miklas PN: GWAS of resistance to three bacterial diseases in the Andean common bean diversity panel. Front Plant Sci. 2024 Sep 5;15:1469381. doi: 10.3389/fpls.2024.1469381.  eCollection 2024. [PubMed:39301162  ] 
  3. Sandor L, Donka T, Barath B, Javor P, Jasz DK, Perenyi D, Babik B, Varga E, Torok L, Hartmann P: Mitochondrial dysfunction in platelets from severe trauma patients - A prospective case-control study. Injury. 2024 Sep;55 Suppl 3:111481. doi: 10.1016/j.injury.2024.111481. Epub 2024  Sep 17. [PubMed:39300624  ] 
  4. Weijers SA, Vermeulen M, Kliza KW: The quest to identify ADP-ribosylation readers: methodological advances. Trends Biochem Sci. 2024 Sep 19:S0968-0004(24)00205-6. doi:  10.1016/j.tibs.2024.08.006. [PubMed:39304454  ] 
  5. Wang T, Niu B, Xu N, Zhang L: ADP-based online compensation hierarchical sliding-mode control for partially unknown switched nonlinear systems with actuator failures. ISA Trans. 2024 Sep 10:1-13. doi: 10.1016/j.isatra.2024.09.011. [PubMed:39304368  ] 
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  7. Astrom LM, Sibolt P, Chamberlin H, Serup-Hansen E, Andersen CE, van Herk M, Mouritsen LS, Aznar MC, Behrens CP: Artificial intelligence-generated targets and inter-observer variation in online adaptive radiotherapy of bladder cancer. Phys Imaging Radiat Oncol. 2024 Sep 1;31:100640. doi: 10.1016/j.phro.2024.100640.  eCollection 2024 Jul. [PubMed:39297081  ] 
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