7M03

Target information

RCSB PDB
7M03
Title
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 18c
Method
X-RAY DIFFRACTION
Resolution
2
Classification
HYDROLASE/INHIBITOR
Organism
Severe acute respiratory syndrome coronavirus 2
Protein
Replicase polyprotein 1ab (P0DTD1)    Looking for covalent inhibitors of this target ?
Year
2021
Publication Title
Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
Abstract

The COVID-19 pandemic is having a major impact on public health worldwide, and there is an urgent need for the creation of an armamentarium of effective therapeutics, including vaccines, biologics, and small-molecule therapeutics, to combat SARS-CoV-2 and emerging variants. Inspection of the virus life cycle reveals multiple viral- and host-based choke points that can be exploited to combat the virus. SARS-CoV-2 3C-like protease (3CLpro), an enzyme essential for viral replication, is an attractive target for therapeutic intervention, and the design of inhibitors of the protease may lead to the emergence of effective SARS-CoV-2-specific antivirals. We describe herein the results of our studies related to the application of X-ray crystallography, the Thorpe-Ingold effect, deuteration, and stereochemistry in the design of highly potent and nontoxic inhibitors of SARS-CoV-2 3CLpro.

External Link
RCSB PDB





Ligand information

HET
YLD
Chain ID
A
HET Number
401
Molecular Formula
C21H30FN3O8S
Structure
2D structure
IUPAC Name
(2S)-2-[[(2S)-2-[(3-fluorophenyl)methoxycarbonylamino]-4-methyl-pentanoyl]amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
InChI
InChI=1S/C21H30FN3O8S/c1-12(2)8-16(25-21(29)33-11-13-4-3-5-15(22)9-13)19(27)24-17(20(28)34(30,31)32)10-14-6-7-23-18(14)26/h3-5,9,12,14,16-17,20,28H,6-8,10-11H2,1-2H3,(H,23,26)(H,24,27)(H,25,29)(H,30,31,32)/t14-,16-,17-,20?/m0/s1
InChI Key
LNGFVEUFXDACOC-YQASGENESA-N
Canonical SMILES
CC(C)C[C@H](NC(=O)OCc1cccc(F)c1)C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O
Bioactivity data
CI006822

Covalent Binding

Warhead
Sulfonic acid
Reaction Mechanism
Nucleophilic Substitution
Residue
CYS : 145
Residue Chain
A
Interactions
Pharmacophore Model