Modomics - A Database of RNA Modifications

The molecule is shown in a ball-and-stick representation with the following colors for atoms :
Hydrogen (H): white Carbon (C): gray Oxygen (O): red Phosphorus (P): orange Nitrogen (N): blue Selenium (Se): gold Sulfur (S): yellow

Summary

Full nameadenosine-5'-diphosphate
IUPAC name[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-oxidophosphoryl] phosphate
Short nameppA
MODOMICS code new2000000552A
MODOMICS code552A
Synonyms
20398-34-9
2e2p
2fr8
2hmv
2ja3
2o1v
2qv7
[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-phosphoryl] phosphate
[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-2-oxolanyl]methoxy-oxidophosphoryl] phosphate
[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-oxidophosphoryl] phosphate
2r6f
2rio
2vhj
2y8i
2y8l
2y8q
2z4r
2zfi
2zkj
3a1d
3atu
3atv
3ay9
3bf1
3bxz
3c7n
3cf1
3d2r
3dgn
3i73
3k1j
3llm
3mle
3ncr
3p23
3qc9
3qxh
3rup
3rv3
3rv4
3t4n
3ta1
3tif
4i3z
58-64-0
5'-O-[(phosphonatooxy)phosphinato]adenosine
9-{5-O-[(Phosphonatooxy)phosphinato]pentofuranosyl}-9H-purin-6-amine
A831962
AC1OEJTD
Adenosine 5'-diphosphate
adenosine 5'-pyrophosphate
adenosine pyrophosphate
adenosine-5-diphosphate
adenosine-5'-diphosphate
adenosine-diphosphate
ADP
ADP trianion
ADP(3-)
CHEBI:456216
CID7058055
DTXSID70942564
Q27225748
ZINC03861153
Nature of the modified residueNatural
RNAMods code
Residue unique ID317
Found in RNAYes
Related nucleosides109

Chemical information

Sum formulaC10H12N5O10P2
Type of moietynucleotide
Degeneracynot aplicable
SMILES[O-][P@@](OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)[n]1c[n]c2c1[n]c[n]c2N)(OP([O-])(=O)[O-])=O
logP0.1498
TPSA260.71
Number of atoms27
Number of Hydrogen Bond Acceptors 1 (HBA1)11
Number of Hydrogen Bond Acceptors 2 (HBA2)15
Number of Hydrogen Bond Donors (HBD)3
PDB exact match , link to the most similar ligand ADP
InChIInChI=1S/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)/p-3/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-K
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs

* Chemical properties calculated with Open Babel - O'Boyle et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011) (link)


Download Structures

2D   .png .mol .mol2 .sdf .pdb .smi
3D   .mol .mol2 .sdf .pdb

Tautomers

Tautomers SMILES
[O-]P(OCC1OC(C(O)C1O)n2cnc3c2ncnc3N)(OP([O-])(=O)[O-])=O tautomer #0
[O-]P(OCC1OC(C(O)C1O)n2cnc3c2ncnc3N)(OP([O-])(=O)[O-])=O tautomer #1
[O-]P(OCC1OC(C(O)C1O)n2cnc3c2[nH]cnc3=N)(OP([O-])(=O)[O-])=O tautomer #2
[O-]P(OCC1OC(C(O)C1O)n2cnc3c2nc[nH]c3=N)(OP([O-])(=O)[O-])=O tautomer #3
[O-]P(OCC1OC(C(O)C1O)N2C=NC3C2=NC=NC3=N)(OP([O-])(=O)[O-])=O tautomer #4
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
ppA ppA ppA

* CYP Metabolic sites predicted with SMARTCyp. SMARTCyp is a method for prediction of which sites in a molecule that are most liable to metabolism by Cytochrome P450. It has been shown to be applicable to metabolism by the isoforms 1A2, 2A6, 2B6, 2C8, 2C19, 2E1, and 3A4 (CYP3A4), and specific models for the isoform 2C9 (CYP2C9) and isoform 2D6 (CYP2D6). CYP3A4, CYP2D6, and CYP2C9 are the three of the most important enzymes in drug metabolism since they are involved in the metabolism of more than half of the drugs used today. The three top-ranked atoms are highlighted. See: SmartCYP and SmartCYP - background; Patrik Rydberg, David E. Gloriam, Lars Olsen, The SMARTCyp cytochrome P450 metabolism prediction server, Bioinformatics, Volume 26, Issue 23, 1 December 2010, Pages 2988–2989 (link)


LC-MS Information

Monoisotopic massNone
Average mass424.177
[M+H]+ not available
Product ions not available
Normalized LC elution time * not available
LC elution order/characteristics not available

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.

Last modification of this entry: Sept. 22, 2023