Modomics - A Database of RNA Modifications

preQ0base
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 name7-cyano-7-carbaguanine
Short namepreQ0base
MODOMICS code new200100000G
MODOMICS code100000G
Nature of the modified residueNatural
RNAMods codeψ
Residue unique ID95
Found in RNAYes
Found in phylogenyArchaea, Eubacteria

Chemical information

Sum formulaC7H5N5O
Type of moietybase
Degeneracynot applicable
SMILESNc1[nH]c(=O)c2c(c[nH]c2n1)C#N
logP0.28628
TPSA111.35
Number of atoms13
Number of Hydrogen Bond Acceptors 1 (HBA1)4
Number of Hydrogen Bond Acceptors 2 (HBA2)4
Number of Hydrogen Bond Donors (HBD)3
PDB no exac match , link to the most similar ligand PQ0
PDB exact match , link to the most similar ligand PQ0
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C7H5N5O/c8-1-3-2-10-5-4(3)6(13)12-7(9)11-5/h2H,(H4,9,10,11,12,13)
InChIKeyFMKSMYDYKXQYRV-UHFFFAOYSA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 

* 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
N=c1[nH]c(=O)c2c(c[nH]c2[nH]1)C#N tautomer #0
Nc1nc(O)c-2c(cnc2[nH]1)C#N tautomer #1
Nc1nc(O)c2c(c[nH]c2n1)C#N tautomer #2
Nc1nc(=O)c2c(c[nH]c2[nH]1)C#N tautomer #3
Nc1[nH]c(O)c-2c(cnc2n1)C#N tautomer #4
Nc1[nH]c(=O)c2c(c[nH]c2n1)C#N tautomer #5
Nc1nc(O)c2C(C=Nc2n1)C#N tautomer #6
N=C1NC(O)C2=C(C=NC2=N1)C#N tautomer #7
N=c1[nH]c(=O)c2=C(CN=c2[nH]1)C#N tautomer #8
N=C1NC(=O)C2C(C=NC2=N1)C#N tautomer #9
NC1=NC(=O)C2=C(C=NC2N1)C#N tautomer #10
N=c1[nH]c(O)c2c(c[nH]c2n1)C#N tautomer #11
N=C1NC(=O)C2C(=CN=C2N1)C#N tautomer #12
N=c1[nH]c(=O)c2C(C=Nc2[nH]1)C#N tautomer #13
Nc1nc(O)c2c(c[nH]c2n1)C#N tautomer #14
NC1=NC(O)C2=C(C=NC2=N1)C#N tautomer #15
Nc1nc(=O)c2=C(CN=c2[nH]1)C#N tautomer #16
N=C1NC(=O)C2=C(CNC2=N1)C#N tautomer #17
NC1=NC(=O)C2C(C=NC2=N1)C#N tautomer #18
N=C1NC(=O)C2=C(C=NC2N1)C#N tautomer #19
NC1=NC(=O)C2C(=CN=C2N1)C#N tautomer #20
N=C1NC(=O)C2C(=CNC2=N1)C#N tautomer #21
Nc1nc(=O)c2C(C=Nc2[nH]1)C#N tautomer #22
Nc1nc(O)c2=C(CN=c2n1)C#N tautomer #23
NC1=NC(=O)C2=C(CNC2=N1)C#N tautomer #24
Nc1[nH]c(=O)c2=C(CN=c2n1)C#N tautomer #25
Nc1[nH]c(=O)c2C(C=Nc2n1)C#N tautomer #26
NC=1NC(=O)C2=C(C=NC2N1)C#N tautomer #27
N=c1nc(O)c2c(c[nH]c2[nH]1)C#N tautomer #28
NC1=NC(=O)C2C(=CNC2=N1)C#N tautomer #29
NC=1NC(=O)C2C(=CN=C2N1)C#N tautomer #30
Nc1nc(O)c2C(C=Nc2n1)C#N tautomer #31
N=c1[nH]c(O)c2C(C=Nc2n1)C#N tautomer #32
N=c1[nH]c(O)c-2c(cnc2[nH]1)C#N tautomer #33
N=c1nc(O)c2=C(CN=c2[nH]1)C#N tautomer #34
N=C1N=C(O)C2C(C=NC2=N1)C#N tautomer #35
N=C1N=C(O)C2=C(C=NC2N1)C#N tautomer #36
N=C1N=C(O)C2C(=CN=C2N1)C#N tautomer #37
N=c1nc(O)c2C(C=Nc2[nH]1)C#N tautomer #38
N=C1N=C(O)C2=C(CNC2=N1)C#N tautomer #39
NC=1N=C(O)C2=C(C=NC2N1)C#N tautomer #40
N=C1N=C(O)C2C(=CNC2=N1)C#N tautomer #41
NC=1N=C(O)C2C(=CN=C2N1)C#N tautomer #42
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
preQ0base preQ0base preQ0base

* 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 mass175.0494
Average mass175.148
[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 starting from 7-cyano-7-carbaguanine

Name
preQ0base:preQ0
preQ0base:preQ1base

Last modification of this entry: Sept. 22, 2023