7T4B

Structure of SARS-CoV-2 3CL protease in complex with inhibitor 14c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.

Dampalla, C.S.Rathnayake, A.D.Galasiti Kankanamalage, A.C.Kim, Y.Perera, K.D.Nguyen, H.N.Miller, M.J.Madden, T.K.Picard, H.R.Thurman, H.A.Kashipathy, M.M.Liu, L.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

(2022) J Med Chem 65: 7818-7832

  • DOI: 10.1021/acs.jmedchem.2c00224
  • Primary Citation of Related Structures:  
    7T3Y, 7T3Z, 7T40, 7T41, 7T42, 7T43, 7T44, 7T45, 7T46, 7T48, 7T49, 7T4A, 7T4B

  • PubMed Abstract: 
  • The worldwide impact of the ongoing COVID-19 pandemic on public health has made imperative the discovery and development of direct-acting antivirals aimed at targeting viral and/or host targets. SARS-CoV-2 3C-like protease (3CL pro ) has emerged as a validated target for the discovery of SARS-CoV-2 therapeutics because of the pivotal role it plays in viral replication ...

    The worldwide impact of the ongoing COVID-19 pandemic on public health has made imperative the discovery and development of direct-acting antivirals aimed at targeting viral and/or host targets. SARS-CoV-2 3C-like protease (3CL pro ) has emerged as a validated target for the discovery of SARS-CoV-2 therapeutics because of the pivotal role it plays in viral replication. We describe herein the structure-guided design of highly potent inhibitors of SARS-CoV-2 3CL pro that incorporate in their structure novel spirocyclic design elements aimed at optimizing potency by accessing new chemical space. Inhibitors of both SARS-CoV-2 3CL pro and MERS-CoV 3CL pro that exhibit nM potency and high safety indices have been identified. The mechanism of action of the inhibitors and the structural determinants associated with binding were established using high-resolution cocrystal structures.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA, B309Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FWI (Subject of Investigation/LOI)
Query on FWI

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
(1R,2S)-2-{[N-({[1-(tert-butoxycarbonyl)azetidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]propane-1-sulfonic acid
C23 H38 N4 O10 S
WDYXMIZDWOFVQK-HTCLRFROSA-N
 Ligand Interaction
FZI (Subject of Investigation/LOI)
Query on FZI

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
(1S,2S)-2-{[N-({[1-(tert-butoxycarbonyl)azetidin-3-yl]methoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]propane-1-sulfonic acid
C23 H38 N4 O10 S
WDYXMIZDWOFVQK-HTCLRFROSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.418α = 90
b = 99.032β = 108.2
c = 59.111γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI161085

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Structure summary
  • Version 1.2: 2022-06-08
    Changes: Database references
  • Version 1.3: 2022-06-15
    Changes: Database references