Modomics - A Database of RNA Modifications

NADpN
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 name5' nicotinamide adenine dinucleotide
Short nameNADpN
MODOMICS code new2000000255N
MODOMICS code255N
Nature of the modified residueNatural
RNAMods codeΞ
Residue unique ID154
Found in RNAYes

Chemical information

Sum formulaC26H33N7O20P3
Type of moietynucleotide
Degeneracyunspecified residue
SMILESNC(c1ccc[n+]([C@@H]2O[C@H](COP([O-])(OP([O-])(OC[C@H]3O[C@@H]([n]4cnc5c(N)ncnc45)[C@H](O)[C@@H]3OP([O-])(OC[C@H]3O[C@@H]%91[C@H](O)[C@@H]3O)=O)=O)=O)[C@@H](O)[C@H]2O)c1)=O.[*]%91
logP-0.8626
TPSA441.4
Number of atoms57
Number of Hydrogen Bond Acceptors 1 (HBA1)23
Number of Hydrogen Bond Acceptors 2 (HBA2)26
Number of Hydrogen Bond Donors (HBD)7
PDB no exac match , link to the most similar ligand 8NA
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChI
InChIKey

* 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
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(N)ncnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #0
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(N)ncnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #1
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(N)ncnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #2
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(N)ncnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #3
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(=N)nc[nH]c45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #4
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(=N)[nH]cnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #5
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(=N)nc[nH]c45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #6
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(=N)[nH]cnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #7
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(N)ncnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #8
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(N)ncnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #9
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(N)ncnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #10
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(N)ncnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #11
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(N4C=NC5C(=N)N=CN=C45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #12
NC(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(N4C=NC5C(=N)N=CN=C45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)=O tautomer #13
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(=N)nc[nH]c45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #14
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(=N)[nH]cnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #15
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(=N)nc[nH]c45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #16
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(n4cnc5c(=N)[nH]cnc45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #17
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(N4C=NC5C(=N)N=CN=C45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #18
N=C(c1ccc[n+](C2OC(COP([O-])(OP([O-])(OCC3OC(N4C=NC5C(=N)N=CN=C45)C(O)C3OP([O-])(OCC6OC(C(O)C6O)*)=O)=O)=O)C(O)C2O)c1)O tautomer #19
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
NADpN NADpN NADpN

* 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 mass661.0935
Average mass856.496
[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.

Reactions producing 5' nicotinamide adenine dinucleotide

Name
pppN:NADpN

Publications

Title Authors Journal Details PubMed Id DOI
Giardia lamblia RNA cap guanine-N2 methyltransferase (Tgs2). Hausmann S, Shuman S J Biol Chem [details] 16046409 -

Last modification of this entry: Sept. 22, 2023