6LKA | pdb_00006lka

Crystal Structure of EV71-3C protease with a Novel Macrocyclic Compounds

• PDB DOI: https://doi.org/10.2210/pdb6LKA/pdb

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


• Deposited: 2019-12-18 Released: 2020-06-17 
• Deposition Author(s): Li, P., Wu, S.Q., Xiao, T.Y.C., Li, Y.L., Su, Z.M., Hao, F., Hu, G.P., Hu, J., Lin, F.S., Chen, X.S., Gu, Z.X., He, H.Y., Li, J., Chen, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.259 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis, and evaluation of a novel macrocyclic anti-EV71 agent.

Li, P., Wu, S., Xiao, T., Li, Y., Su, Z., Wei, W., Hao, F., Hu, G., Lin, F., Chen, X., Gu, Z., Lin, T., He, H., Li, J., Chen, S.

(2020) Bioorg Med Chem 28: 115551-115551

• PubMed: 32503695 
• DOI: https://doi.org/10.1016/j.bmc.2020.115551
• Primary Citation Related Structures: 
  6LKA


• PubMed Abstract: 
  

  We describe here the design, synthesis, and evaluation of a macrocyclic peptidomimetic as a potent agent targeting enterovirus A71 (EV71). The compound has a 15-membered macrocyclic ring in a defined conformation. Yamaguchi esterification reaction was used to close the 15-membered macrocycle instead of the typical Ru-catalyzed ring-closing olefin metathesis reaction. The crystallographic characterization of the complex between this compound and its target, 3C protease from EV71, validated the design and paved the way for the generation of a new series of anti-EV71 agents.

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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; Cancer Research Center of Xiamen University, Xiamen, Fujian, China; State Key Laboratory of Drug Lead Compound Research, WuXi AppTec (Shanghai) Co., Ltd., Shanghai, China.
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; Cancer Research Center of Xiamen University, Xiamen, Fujian, China.
State Key Laboratory of Drug Lead Compound Research, WuXi AppTec (Shanghai) Co., Ltd., Shanghai, China.
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; Cancer Research Center of Xiamen University, Xiamen, Fujian, China. Electronic address: [e-mail].
State Key Laboratory of Drug Lead Compound Research, WuXi AppTec (Shanghai) Co., Ltd., Shanghai, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.61 kDa 
• Atom Count: 1,565 
• Modeled Residue Count: 181 
• Deposited Residue Count: 181 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C proteinase	A	181	Enterovirus A71	Mutation(s): 0  EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
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
EGF	B [auth A]	~{N}-[(2~{S})-1-[[(2~{S},3~{S},6~{S},7~{Z},12~{E})-4,9-bis(oxidanylidene)-6-[[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]methyl]-2-phenyl-1,10-dioxa-5-azacyclopentadeca-7,12-dien-3-yl]amino]-3-methyl-1-oxidanylidene-butan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide C33 H41 N5 O8 XPQNIWALCQRNAP-GPCDZKPZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.259 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.27	α = 90
b = 64.641	β = 90
c = 75.855	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
AUTOMAR	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Li, P., Wu, S.Q., Xiao, T.Y.C., Li, Y.L., Su, Z.M., Hao, F., Hu, G.P., Hu, J., Lin, F.S., Chen, X.S., Gu, Z.X., He, H.Y., Li, J., Chen, S.H.

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary