5BPE | pdb_00005bpe

Crystal structure of EV71 3Cpro in complex with a potent and selective Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5BPE/pdb

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


• Deposited: 2015-05-28 Released: 2015-11-25 
• Deposition Author(s): Luqing, S., Yin, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.281 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Cyanohydrin as an Anchoring Group for Potent and Selective Inhibitors of Enterovirus 71 3C Protease

Zhai, Y., Zhao, X., Cui, Z., Wang, M., Wang, Y., Li, L., Sun, Q., Yang, X., Zeng, D., Liu, Y., Sun, Y., Lou, Z., Shang, L., Yin, Z.

(2015) J Med Chem 58: 9414-9420

• PubMed: 26571192 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01013
• Primary Citation Related Structures: 
  5BPE


• PubMed Abstract: 
  

  Cyanohydrin derivatives as enterovirus 71 (EV71) 3C protease (3C(pro)) inhibitors have been synthesized and assayed for their biochemical and antiviral activities. Compared with the reported inhibitors, cyanohydrins (1S,2S,2'S,5S)-16 and (1R,2S,2'S,5S)-16 exhibited significantly improved activity and attractive selectivity profiles against other proteases, which were a result of the specific interactions between the cyanohydrin moiety and the catalytic site of 3C(pro). Cyanohydrin as an anchoring group with high selectivity and excellent inhibitory activity represents a useful choice for cysteine protease inhibitors.

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Organizational Affiliation: 
• College of Pharmacy and State Key Laboratory of Elemento-Organic Chemistry, Nankai University , 94 Weijin Road, Nankai District, Tianjin 300071, China.
Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300071, China.
Laboratory of Structural Biological & Ministry of Education (MOE), and Laboratory of Protein Science, School of Medicine and Life Sciences, Tsinghua University , Beijing 100084, China.
College of Chemistry, and Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University , Wuhan 430079, China.
National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science , Beijing 100101, China.

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: 20.48 kDa 
• Atom Count: 1,447 
• Modeled Residue Count: 180 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EV71 3Cpro	A	180	Enterovirus A71	Mutation(s): 0
UniProt
Find proteins for A0A0X1KHD2 (Human enterovirus 71) Explore A0A0X1KHD2  Go to UniProtKB:  A0A0X1KHD2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E22	B [auth A]	(2~{S})-~{N}-[(1~{R},2~{S})-1-cyano-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-3-phenyl-2-[[(~{E})-3-phenylprop-2-enoyl]amino]propanamide C27 H30 N4 O4 UJFNOZFDUMAJFU-XSAZPJIKSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002211 (E22)	B [auth A]	(2~{S})-~{N}-[(1~{R},2~{S})-1-cyano-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-3-phenyl-2-[[(~{E})-3-phenylprop-2-enoyl]amino]propanamide	Peptide-like / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.281 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.766	α = 90
b = 63.271	β = 116.97
c = 38.76	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Luqing, S., Yin, Z.

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2015-12-09
  Changes: Database references
• Version 1.2: 2016-01-20
  Changes: Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations