5C5N | pdb_00005c5n

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

• PDB DOI: https://doi.org/10.2210/pdb5C5N/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-06-21 Released: 2016-06-22 
• Deposition Author(s): Akaji, K., Teruya, K., Shimamoto, Y., Sanjho, A., Yamashita, E., Nakagawa, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.321 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.290 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.292 (Depositor) 

Literature

Fused-ring structure of N-decalin as a novel scaffold for SARS 3CL protease inhibitors

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.27 kDa 
• Atom Count: 2,496 
• Modeled Residue Count: 306 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 1  EC: 3.4.22.69
UniProt
Find proteins for P0C6X7 (Severe acute respiratory syndrome coronavirus) Explore P0C6X7  Go to UniProtKB:  P0C6X7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLH	B [auth A]	(2S)-3-(1H-imidazol-5-yl)-2-({[(3R,4aS,8aR)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal C25 H35 N5 O2 HCMRRQNNHUOUJM-NVXDSCFRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.321 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.290 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.292 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.801	α = 90
b = 82.091	β = 104.35
c = 53.266	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data reduction
PDB_EXTRACT	data extraction
MOLREP	model building
Coot	model building
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-22 
Deposition Author(s): Akaji, K., Teruya, K., Shimamoto, Y., Sanjho, A., Yamashita, E., Nakagawa, A.

Revision History  

• Version 1.0: 2016-06-22
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Structure summary