5C5O | pdb_00005c5o

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

• PDB DOI: https://doi.org/10.2210/pdb5C5O/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: 1.50 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.248 (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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.54 kDa 
• Atom Count: 5,161 
• Modeled Residue Count: 600 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B	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
SDJ	C [auth A], D [auth B]	(2S)-3-(1H-imidazol-5-yl)-2-({[(3S,4aR,8aS)-2-(N-phenyl-beta-alanyl)decahydroisoquinolin-3-yl]methyl}amino)propanal C25 H35 N5 O2 HCMRRQNNHUOUJM-CHOVIJNXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.663	α = 93.73
b = 58.662	β = 103.4
c = 68.098	γ = 106.51

Software Package:

Software Name	Purpose
DENZO	data collection
SCALEPACK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	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: 2024-11-20
  Changes: Data collection, Database references, Structure summary