7C7P

Crystal structure of the SARS-CoV-2 main protease in complex with Telaprevir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

SARS-CoV-2 M pro inhibitors with antiviral activity in a transgenic mouse model.

Qiao, J.Li, Y.S.Zeng, R.Liu, F.L.Luo, R.H.Huang, C.Wang, Y.F.Zhang, J.Quan, B.Shen, C.Mao, X.Liu, X.Sun, W.Yang, W.Ni, X.Wang, K.Xu, L.Duan, Z.L.Zou, Q.C.Zhang, H.L.Qu, W.Long, Y.H.Li, M.H.Yang, R.C.Liu, X.You, J.Zhou, Y.Yao, R.Li, W.P.Liu, J.M.Chen, P.Liu, Y.Lin, G.F.Yang, X.Zou, J.Li, L.Hu, Y.Lu, G.W.Li, W.M.Wei, Y.Q.Zheng, Y.T.Lei, J.Yang, S.

(2021) Science 371: 1374-1378

  • DOI: 10.1126/science.abf1611
  • Primary Citation of Related Structures:  
    7C7P, 7COM, 7D3I

  • PubMed Abstract: 
  • The COVID-19 pandemic caused by the SARS-CoV-2 virus continually poses serious threats to global public health. The main protease (M pro ) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing M pro inhibitors derived from either Boceprevir or Telaprevir, both of which are approved antivirals ...

    The COVID-19 pandemic caused by the SARS-CoV-2 virus continually poses serious threats to global public health. The main protease (M pro ) of SARS-CoV-2 plays a central role in viral replication. We designed and synthesized 32 new bicycloproline-containing M pro inhibitors derived from either Boceprevir or Telaprevir, both of which are approved antivirals. All compounds inhibited SARS-CoV-2 M pro activity in vitro with IC 50 values ranging from 7.6 to 748.5 nM. The co-crystal structure of M pro in complex with MI-23, one of the most potent compounds, revealed its interaction mode. Two compounds (MI-09 and MI-30) showed excellent antiviral activity in cell-based assays. In a SARS-CoV-2 infection transgenic mouse model, oral or intraperitoneal treatment with MI-09 or MI-30 significantly reduced lung viral loads and lung lesions. Both also displayed good pharmacokinetic properties and safety in rats.


    Organizational Affiliation

    State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. yangsy@scu.edu.cn leijian@scu.edu.cn zhengyt@mail.kiz.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA, B306Severe 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), 3.1 (UniProt), 2.1.1 (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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SV6 (Subject of Investigation/LOI)
Query on SV6

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
(1S,3aR,6aS)-2-[(2S)-2-({(2S)-2-cyclohexyl-2-[(pyrazin-2-ylcarbonyl)amino]acetyl}amino)-3,3-dimethylbutanoyl]-N-[(2R,3S)-1-(cyclopropylamino)-2-hydroxy-1-oxohexan-3-yl]octahydrocyclopenta[c]pyrrole-1-carboxamide
C36 H55 N7 O6
FTZGWEAUHOMNIG-FJRGXGLZSA-N
 Ligand Interaction
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002448 (SV6)
Query on PRD_002448
C [auth A],
E [auth B]
TELAPREVIR, bound formPeptide-like / Antiviral Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.907α = 90
b = 98.731β = 90
c = 103.487γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2020YFS0010/HX2019nCoV039

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2021-03-10
    Changes: Structure summary
  • Version 2.0: 2021-04-14
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary