Summary

Full name5' (3' -dephospho-CoA)
Short nameCoApN
MODOMICS code455N
Nature of the modified residueNatural
RNAMods code
Residue unique ID149
Found in RNAYes

Chemical information

Sum formulaC26H40N7O19P3S
Type of moietynucleotide
Degeneracyunspecified residue
SMILESCC(C)(COP([O-])(OP([O-])(OC[C@H]1O[C@@H]([n]2cnc3c(N)ncnc23)[C@H](O)[C@@H]1OP([O-])(OC[C@H]1O[C@@H]%91[C@H](O)[C@@H]1O)=O)=O)=O)C(O)C(NCCC(NCCS)=O)=O.[*]%91
logP0.4525
TPSA461.97
Number of atoms57
Number of Hydrogen Bond Acceptors 1 (HBA1)24
Number of Hydrogen Bond Acceptors 2 (HBA2)27
Number of Hydrogen Bond Donors (HBD)8
PDB no exac match , link to the most similar ligand COA
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0001423
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
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(NCCS)=O)O tautomer #0
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(NCCS)=O)O tautomer #1
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(NCCS)=O)=O tautomer #2
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(NCCS)=O)=O tautomer #3
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCC=C(NCCS)O)O tautomer #4
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCC=C(NCCS)O)O tautomer #5
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCC=C(NCCS)O)=O tautomer #6
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCC=C(NCCS)O)=O tautomer #7
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(NCCS)=O)O tautomer #8
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(NCCS)=O)O tautomer #9
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(NCCS)=O)=O tautomer #10
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(NCCS)=O)=O tautomer #11
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(NCCS)=O)O tautomer #12
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(NCCS)=O)O tautomer #13
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(NCCS)=O)O tautomer #14
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(NCCS)=O)O tautomer #15
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(=NCCS)O)O tautomer #16
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(=NCCS)O)O tautomer #17
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(=NCCS)O)=O tautomer #18
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(=NCCS)O)=O tautomer #19
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(NCCS)=O)O tautomer #20
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(NCCS)=O)=O tautomer #21
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCC=C(NCCS)O)O tautomer #22
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCC=C(NCCS)O)O tautomer #23
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCC=C(NCCS)O)=O tautomer #24
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCC=C(NCCS)O)=O tautomer #25
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCC=C(NCCS)O)O tautomer #26
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCC=C(NCCS)O)O tautomer #27
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCC=C(NCCS)O)O tautomer #28
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCC=C(NCCS)O)O tautomer #29
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(NCCS)=O)O tautomer #30
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(NCCS)=O)O tautomer #31
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(NCCS)=O)O tautomer #32
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(NCCS)=O)O tautomer #33
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(=NCCS)O)O tautomer #34
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(=NCCS)O)O tautomer #35
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(=NCCS)O)=O tautomer #36
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(=NCCS)O)=O tautomer #37
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCC=C(NCCS)O)O tautomer #38
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCC=C(NCCS)O)=O tautomer #39
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(=NCCS)O)O tautomer #40
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(=NCCS)O)O tautomer #41
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(=NCCS)O)O tautomer #42
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(N)ncnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(=NCCS)O)O tautomer #43
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(NCCS)=O)O tautomer #44
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(NCCS)=O)O tautomer #45
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(=O)C(NCCC(=NCCS)O)O tautomer #46
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(NCCC(=NCCS)O)=O tautomer #47
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCC=C(NCCS)O)O tautomer #48
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCC=C(NCCS)O)O tautomer #49
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCC=C(NCCS)O)O tautomer #50
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCC=C(NCCS)O)O tautomer #51
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(=NCCS)O)O tautomer #52
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(=NCCS)O)O tautomer #53
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCC=C(NCCS)O)O tautomer #54
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)nc[nH]c23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(=NCCS)O)O tautomer #55
CC(C)(COP([O-])(OP([O-])(OCC1OC(n2cnc3c(=N)[nH]cnc23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(=NCCS)O)O tautomer #56
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCC=C(NCCS)O)O tautomer #57
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)=C(NCCC(=NCCS)O)O tautomer #58
CC(C)(COP([O-])(OP([O-])(OCC1OC(N2C=NC3C(=N)N=CN=C23)C(O)C1OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C(=NCCC(=NCCS)O)O tautomer #59

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
CoApN CoApN CoApN

* 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 mass684.1254
Average mass879.618
[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' (3' -dephospho-CoA)

Name
pppN:CoApN

Reactions starting from 5' (3' -dephospho-CoA)

Name
CoApN:acCoApN
CoApN:malonyl-CoApN
CoApN:succinyl-CoApN

Publications

Title Authors Journal Details PubMed Id DOI
A chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA. Kowtoniuk WE, Shen Y, Heemstra JM, Agarwal I, Liu DR Proc Natl Acad Sci U S A [details] 19416889 -

Last modification of this entry: Sept. 29, 2021


Copyright © Genesilico - All rights reserved
If you have any advice or suggestions for corrections or improvements, please contact: Andrea Cappannini - lp.vog.bcmii@ininnappaca