Modomics - A Database of RNA Modifications

preQ1
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-aminomethyl-7-deazaguanosine
IUPAC name2-amino-5-(aminomethyl)-7-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-pyrrolo[2,3-d]pyrimidin-4-one
Short namepreQ1
MODOMICS code new2000000101G
MODOMICS code101G
Synonyms
2-amino-5-(aminomethyl)-7-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-pyrrolo[2,3-d]pyrimidin-4-one
2-amino-5-(aminomethyl)-7-(|A-d-ribofuranosyl)-1,7-dihydro-4h-pyrrolo[2,3-d]pyrimidin-4-one
4H-Pyrrolo(2,3-d)pyrimidin-4-one, 2-amino-5-(aminomethyl)-1,7-dihydro-7-beta-D-ribofuranosyl-
5-(Aminomethyl)-2-imino-7-pentofuranosyl-2,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-4-ol
66048-70-2
7400-35-3
7-(Aminomethyl)-7-carbaguanosine
7-Aminomethyl-7-deazaguanosine
AC1L4T63
AC1Q6I9T
AR-1D8415
CID191792
DTXSID60984514
Nature of the modified residueNatural
RNAMods code∉
Residue unique ID123
Found in RNAYes
Related nucleotides408
Enzymes Tgt (Escherichia coli)
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC12H17N5O5
Type of moietynucleoside
Degeneracynot applicable
SMILESNc1[nH]c(=O)c2c(CN)c[n]([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c2n1
logP-1.3415
TPSA172.64
Number of atoms22
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)6
PDB no exac match , link to the most similar ligand PQ1
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C12H17N5O5/c13-1-4-2-17(9-6(4)10(21)16-12(14)15-9)11-8(20)7(19)5(3-18)22-11/h2,5,7-8,11,18-20H,1,3,13H2,(H3,14,15,16,21)/t5-,7-,8-,11-/m1/s1
InChIKeySOEYIPCQNRSIAV-IOSLPCCCSA-N
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
N=C1NC(O)c2c(C=N)cn(C3OC(CO)C(O)C3O)c2N1 tautomer #0
N=c1[nH]c(=O)c2c(CN)cn(C3OC(CO)C(O)C3O)c2[nH]1 tautomer #1
Nc1nc(O)c2c(CN)cn(C3OC(CO)C(O)C3O)c2n1 tautomer #2
NC1=NC(O)c2c(C=N)cn(C3OC(CO)C(O)C3O)c2N1 tautomer #3
Nc1nc(=O)c2c(CN)cn(C3OC(CO)C(O)C3O)c2[nH]1 tautomer #4
Nc1[nH]c(=O)c2c(CN)cn(C3OC(CO)C(O)C3O)c2n1 tautomer #5
N=c1[nH]c(O)c2c(CN)cn(C3OC(CO)C(O)C3O)c2n1 tautomer #6
Nc1nc(O)c2C(C=N)CN(C3OC(CO)C(O)C3O)c2n1 tautomer #7
Nc1nc(O)c2C(=CN)CN(C3OC(CO)C(O)C3O)c2n1 tautomer #8
N=C1NC(=O)C2C(C=N)=CN(C3OC(CO)C(O)C3O)C2N1 tautomer #9
N=C1NC(=O)C2=C(C=N)CN(C3OC(CO)C(O)C3O)C2N1 tautomer #10
N=C1NC(=O)C2C(CN)=CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #11
N=C1NC(=O)C2C(C=N)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #12
N=C1NC(O)C2=C(C=N)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #13
N=C1NC(=O)C2=C(CN)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #14
N=c1[nH]c(=O)c2C(C=N)CN(C3OC(CO)C(O)C3O)c2[nH]1 tautomer #15
N=C1NC(=O)C2C(=CN)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #16
N=c1[nH]c(=O)c2C(=CN)CN(C3OC(CO)C(O)C3O)c2[nH]1 tautomer #17
Nc1nc(O)c2c(CN)cn(C3OC(CO)C(O)C3O)c2n1 tautomer #18
NC1=NC(=O)C2C(C=N)=CN(C3OC(CO)C(O)C3O)C2N1 tautomer #19
NC1=NC(=O)C2=C(C=N)CN(C3OC(CO)C(O)C3O)C2N1 tautomer #20
NC1=NC(=O)C2C(CN)=CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #21
NC1=NC(=O)C2C(C=N)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #22
NC1=NC(O)C2=C(C=N)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #23
NC1=NC(=O)C2=C(CN)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #24
Nc1nc(=O)c2C(C=N)CN(C3OC(CO)C(O)C3O)c2[nH]1 tautomer #25
NC1=NC(=O)C2C(=CN)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #26
N=c1nc(O)c2c(CN)cn(C3OC(CO)C(O)C3O)c2[nH]1 tautomer #27
Nc1nc(=O)c2C(=CN)CN(C3OC(CO)C(O)C3O)c2[nH]1 tautomer #28
N=C1NC(O)=C2C(C=N)=CN(C3OC(CO)C(O)C3O)C2N1 tautomer #29
N=c1[nH]c(O)c2C(C=N)CN(C3OC(CO)C(O)C3O)c2n1 tautomer #30
N=c1[nH]c(O)c2C(=CN)CN(C3OC(CO)C(O)C3O)c2n1 tautomer #31
NC1=NC(O)=C2C(C=N)=CN(C3OC(CO)C(O)C3O)C2N1 tautomer #32
N=C1N=C(O)C2C(C=N)=CN(C3OC(CO)C(O)C3O)C2N1 tautomer #33
N=C1N=C(O)C2=C(C=N)CN(C3OC(CO)C(O)C3O)C2N1 tautomer #34
N=C1N=C(O)C2C(CN)=CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #35
N=C1N=C(O)C2C(C=N)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #36
N=C1N=C(O)C2=C(CN)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #37
N=c1nc(O)c2C(C=N)CN(C3OC(CO)C(O)C3O)c2[nH]1 tautomer #38
N=C1N=C(O)C2C(=CN)CN(C3OC(CO)C(O)C3O)C2=N1 tautomer #39
N=c1nc(O)c2C(=CN)CN(C3OC(CO)C(O)C3O)c2[nH]1 tautomer #40
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
preQ1 preQ1 preQ1

* 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 mass311.123
Average mass311.294
[M+H]+312.1308
Product ions180
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.

Chemical groups contained

TypeSubtype
methyl groupmethyl at aromatic C
otherprimary amine

Reactions producing 7-aminomethyl-7-deazaguanosine

Name
preQ1base:preQ1

Reactions starting from 7-aminomethyl-7-deazaguanosine

Name
preQ1:oQ

Last modification of this entry: Sept. 22, 2023