4TWW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


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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:  
    4WY3, 4TWW, 4TWY

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA, B306Severe acute respiratory syndrome-related coronavirusMutation(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), 2.1.1 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus)
Explore P0C6X7 
Go to UniProtKB:  P0C6X7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3A7 (Subject of Investigation/LOI)
Query on 3A7

Download Ideal Coordinates CCD File 
C [auth A], D [auth B](2S)-2-({[(3S,4aR,8aS)-2-(4-bromobenzoyl)decahydroisoquinolin-3-yl]methyl}amino)-3-(1H-imidazol-5-yl)propanal
C23 H29 Br N4 O2
SKLHMRHVVDDIOX-UBBRYJJRSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3A7 Binding MOAD:  4TWW IC50: 6.30e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.89α = 93.11
b = 59.516β = 102.82
c = 68.401γ = 107.3
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPmodel building
HKLdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release