Structure of SARS-3CL protease complex with a phenylbenzoyl (R,S)-N-decalin type inhibitor

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors.

Shimamoto, Y.Hattori, Y.Kobayashi, K.Teruya, K.Sanjoh, A.Nakagawa, A.Yamashita, E.Akaji, K.

(2015) Bioorg Med Chem 23: 876-890

  • DOI: https://doi.org/10.1016/j.bmc.2014.12.028
  • Primary Citation of Related Structures:  
    4TWW, 4TWY, 4WY3

  • PubMed Abstract: 

    The design and evaluation of a novel decahydroisoquinolin scaffold as an inhibitor for severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro)) are described. Focusing on hydrophobic interactions at the S2 site, the decahydroisoquinolin scaffold was designed by connecting the P2 site cyclohexyl group of the substrate-based inhibitor to the main-chain at the α-nitrogen atom of the P2 position via a methylene linker. Starting from a cyclohexene enantiomer obtained by salt resolution, trans-decahydroisoquinolin derivatives were synthesized. All decahydroisoquinolin inhibitors synthesized showed moderate but clear inhibitory activities for SARS 3CL(pro), which confirmed the fused ring structure of the decahydroisoquinolin functions as a novel scaffold for SARS 3CL(pro) inhibitor. X-ray crystallographic analyses of the SARS 3CL(pro) in a complex with the decahydroisoquinolin inhibitor revealed the expected interactions at the S1 and S2 sites, as well as additional interactions at the N-substituent of the inhibitor.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome-related coronavirusMutation(s): 1 
Gene Names: rep1a-1b
EC: 3.4.22
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6X7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 3X5

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-({[(3R,4aS,8aR)-2-(biphenyl-4-ylcarbonyl)decahydroisoquinolin-3-yl]methyl}amino)-3-(1H-imidazol-5-yl)propanal
C29 H34 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
3X5 Binding MOAD:  4WY3 IC50: 2.40e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.89 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.106α = 90
b = 81.82β = 104.69
c = 53.243γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata reduction
MOLREPmodel building
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description