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



Literature

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

Qiao, J.X.Zeng, R.Wang, Y.F.Li, Y.S.Yao, R.Zhou, Y.L.Chen, P.Lei, J.Yang, S.Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
main proteaseAB306Severe 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)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SV6
Query on SV6

Download Ideal Coordinates CCD File 
A
(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
FK3
Query on FK3

Download Ideal Coordinates CCD File 
B
(3~{S},3~{a}~{S},6~{a}~{R})-~{N}-[(2~{R},3~{S})-1-(cyclopropylamino)-2-oxidanyl-1-oxidanylidene-hexan-3-yl]-2-methanoyl-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide
C18 H29 N3 O4
QNPKORKCVLMDCG-VLVIQNCWSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A, 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
ATELAPREVIR, bound formPeptide-like /  Antiviral

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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



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release