4TWY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.290 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.bmc.2014.12.028
  • Primary Citation of Related Structures:  

  • 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 decahydroiso ...

    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. Electronic address: akaji@mb.kyoto-phu.ac.jp.,Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan.,Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Sakyo-ku, Kyoto 606-0823, Japan.,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.,R&D Center, Protein Wave Co., Nara 631-0006, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3C-like proteinase
A
306Human SARS coronavirusMutation(s): 0 
Gene Names: rep
Find proteins for P0C6X7 (Human SARS coronavirus)
Go to UniProtKB:  P0C6X7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3BL
Query on 3BL

Download SDF File 
Download CCD File 
A
(2S)-2-({[(3S,4aR,8aS)-2-(biphenyl-4-ylcarbonyl)decahydroisoquinolin-3-yl]methyl}amino)-3-(1H-imidazol-5-yl)propanal
C29 H34 N4 O2
VZCULZJNALRGNB-CZJMETBBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.290 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.834α = 90.00
b = 82.128β = 104.98
c = 53.271γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
MOLREPmodel building
DENZOdata reduction
DENZOdata collection
SCALEPACKdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2020-01-29
    Type: Data collection, Database references, Derived calculations, Source and taxonomy