7NW2

Crystal Structure of SARS-CoV-2 main protease in complex with LON-WEI-adc59df6-47


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 M pro inhibitor.

Zaidman, D.Gehrtz, P.Filep, M.Fearon, D.Gabizon, R.Douangamath, A.Prilusky, J.Duberstein, S.Cohen, G.Owen, C.D.Resnick, E.Strain-Damerell, C.Lukacik, P.Barr, H.Walsh, M.A.von Delft, F.London, N.

(2021) Cell Chem Biol 28: 1795-1806.e5

  • DOI: https://doi.org/10.1016/j.chembiol.2021.05.018
  • Primary Citation of Related Structures:  
    7NW2

  • PubMed Abstract: 

    Designing covalent inhibitors is increasingly important, although it remains challenging. Here, we present covalentizer, a computational pipeline for identifying irreversible inhibitors based on structures of targets with non-covalent binders. Through covalent docking of tailored focused libraries, we identify candidates that can bind covalently to a nearby cysteine while preserving the interactions of the original molecule. We found ∼11,000 cysteines proximal to a ligand across 8,386 complexes in the PDB. Of these, the protocol identified 1,553 structures with covalent predictions. In a prospective evaluation, five out of nine predicted covalent kinase inhibitors showed half-maximal inhibitory concentration (IC 50 ) values between 155 nM and 4.5 μM. Application against an existing SARS-CoV M pro reversible inhibitor led to an acrylamide inhibitor series with low micromolar IC 50 values against SARS-CoV-2 M pro . The docking was validated by 12 co-crystal structures. Together these examples hint at the vast number of covalent inhibitors accessible through our protocol.


  • Organizational Affiliation

    Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
USZ (Subject of Investigation/LOI)
Query on USZ

Download Ideal Coordinates CCD File 
C [auth A]~{N}-(4-~{tert}-butylphenyl)-~{N}-[(1~{R})-2-[2-(3-fluorophenyl)ethylamino]-2-oxidanylidene-1-pyridin-3-yl-ethyl]propanamide
C28 H32 F N3 O2
KGVPRQJQXHIIJH-AREMUKBSSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.449α = 90
b = 99.748β = 90
c = 103.605γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
REFMACrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-12-29
    Changes: Database references
  • Version 1.2: 2022-12-21
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary