5C1Y | pdb_00005c1y

Crystal structure of EV71 3C Proteinase in complex with Compound 1

• PDB DOI: https://doi.org/10.2210/pdb5C1Y/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Enterovirus A71
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-15 Released: 2016-06-01 
• Deposition Author(s): Zhang, L., Huang, G., Cai, Q., Zhao, C., Ren, H., Li, P., Li, N., Chen, S., Li, J., Lin, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.290 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Optimize the interactions at S4 with efficient inhibitors targeting 3C proteinase from enterovirus 71

Zhang, L., Huang, G., Cai, Q., Zhao, C., Tang, L., Ren, H., Li, P., Li, N., Huang, J., Chen, X., Guan, Y., You, H., Chen, S., Li, J., Lin, T.

(2016) J Mol Recognit 29: 520-527

• PubMed: 27185390 
• DOI: https://doi.org/10.1002/jmr.2551
• Primary Citation Related Structures: 
  5C1U, 5C1X, 5C1Y, 5C20


• PubMed Abstract: 
  

  Enterovirus 71 (EV71) is the causative agent of hand, foot and mouth disease and can spread its infections to the central nervous and other systems with severe consequences. The replication of EV71 depends on its 3C proteinase (3C ^pro ), a significant drug target. By X-ray crystallography and functional assays, the interactions between inhibitors and EV71 3C ^pro were evaluated. It was shown that improved interactions at S4 for the substrate binding could significantly enhance the potency. A new series of potent inhibitors with high ligand efficiency was generated for developing antivirals to treat and control the EV71-associated diseases. Copyright © 2016 John Wiley & Sons, Ltd.

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Organizational Affiliation: 
• State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian, China.
State Key Laboratory on Lead Compound Research, WuXi AppTech Co., Ltd., Shanghai, 200131, China.
Xianmen Center for Disease Control and Prevention, Shen-guang Road 681-685, Xiamen, 361021, China.
Xiamen Hospital of Traditional Chinese Medicine, Xiamen, 361001, China.
Fujian University for Traditional Chinese Medicine, Fuzhou, 350004, China.
State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China.
State Key Laboratory on Lead Compound Research, WuXi AppTech Co., Ltd., Shanghai, 200131, China. [e-mail].
State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.78 kDa 
• Atom Count: 1,486 
• Modeled Residue Count: 181 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C proteinase	A	192	Enterovirus A71	Mutation(s): 0  EC: 3.4.22.28
UniProt
Find proteins for A9XG43 (Human enterovirus 71) Explore A9XG43  Go to UniProtKB:  A9XG43

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GHY	B [auth A]	propan-2-yl N-[(2S)-1-oxidanylidene-1-[[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-3-phenyl-propan-2-yl]carbamate C20 H29 N3 O5 DESRATCONZEYFJ-ULQDDVLXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.290 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.367	α = 90
b = 65.062	β = 90
c = 75.862	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Zhang, L., Huang, G., Cai, Q., Zhao, C., Ren, H., Li, P., Li, N., Chen, S., Li, J., Lin, T.

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2016-10-26
  Changes: Database references
• Version 2.0: 2020-09-02
  Changes: Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-11-06
  Changes: Structure summary