6LKA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.bmc.2020.115551
  • Primary Citation of 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C proteinase181Enterovirus A71Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9XG43
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EGF
Query on EGF

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.202 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.27α = 90
b = 64.641β = 90
c = 75.855γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
AUTOMARdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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