7UR9

SARS-Cov2 Main protease in complex with inhibitor CDD-1845


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors.

Jimmidi, R.Chamakuri, S.Lu, S.Ucisik, M.N.Chen, P.J.Bohren, K.M.Moghadasi, S.A.Versteeg, L.Nnabuife, C.Li, J.Y.Qin, X.Chen, Y.C.Faver, J.C.Nyshadham, P.Sharma, K.L.Sankaran, B.Judge, A.Yu, Z.Li, F.Pollet, J.Harris, R.S.Matzuk, M.M.Palzkill, T.Young, D.W.

(2023) Commun Chem 6: 164-164

  • DOI: https://doi.org/10.1038/s42004-023-00961-y
  • Primary Citation of Related Structures:  
    7UR9, 7URB, 7US4

  • PubMed Abstract: 

    The development of SARS-CoV-2 main protease (M pro ) inhibitors for the treatment of COVID-19 has mostly benefitted from X-ray structures and preexisting knowledge of inhibitors; however, an efficient method to generate M pro inhibitors, which circumvents such information would be advantageous. As an alternative approach, we show here that DNA-encoded chemistry technology (DEC-Tec) can be used to discover inhibitors of M pro . An affinity selection of a 4-billion-membered DNA-encoded chemical library (DECL) using M pro as bait produces novel non-covalent and non-peptide-based small molecule inhibitors of M pro with low nanomolar K i values. Furthermore, these compounds demonstrate efficacy against mutant forms of M pro that have shown resistance to the standard-of-care drug nirmatrelvir. Overall, this work demonstrates that DEC-Tec can efficiently generate novel and potent inhibitors without preliminary chemical or structural information.


  • Organizational Affiliation

    Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase nsp5
A, B
306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O5F
Query on O5F

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2P)-2-(isoquinolin-4-yl)-1-[4-(methylamino)-4-oxobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide
C34 H31 N5 O2
CTPLSMAVLSTZPJ-QFIPXVFZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.72α = 90
b = 100.46β = 90
c = 104.49γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP20CA221729

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references