8CZW

Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 15d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 15d

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

To be published.

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), 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P8L
Query on P8L

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{R},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate
C24 H42 N3 O8 S
BNNIGFVXMNVYNU-HUWCRECTSA-P
 Ligand Interaction
P8U
Query on P8U

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate
C24 H42 N3 O8 S
BNNIGFVXMNVYNU-MWOXCZGJSA-P
 Ligand Interaction
PG4
Query on PG4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.171α = 90
b = 98.526β = 108.03
c = 59.142γ = 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: 2022-06-22
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references, Structure summary