Crystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 1 in complex with a piperidine-thienopyridine derivative

Experimental Data Snapshot

  • Resolution: 1.44 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

Starting Model: experimental
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Structural dissection reveals a general mechanistic principle for group II chitinase (ChtII) inhibition.

Chen, W.Zhou, Y.Yang, Q.

(2019) J Biol Chem 294: 9358-9364

  • DOI: https://doi.org/10.1074/jbc.RA119.007812
  • Primary Citation of Related Structures:  
    6JAV, 6JAW, 6JAX, 6JAY

  • PubMed Abstract: 

    Small-molecule inhibitors of insect chitinases have potential applications for controlling insect pests. Insect group II chitinase (ChtII) is the most important chitinase in insects and functions throughout all developmental stages. However, the possibility of inhibiting ChtII by small molecules has not been explored yet. Here, we report the structural characteristics of four molecules that exhibited similar levels of inhibitory activity against Of ChtII, a group II chitinase from the agricultural pest Asian corn borer Ostrinia furnacalis These inhibitors were chitooctaose ((GlcN) 8 ), dipyrido-pyrimidine derivative (DP), piperidine-thienopyridine derivative (PT), and naphthalimide derivative (NI). The crystal structures of the Of ChtII catalytic domain complexed with each of the four inhibitors at 1.4-2.0 Å resolutions suggested they all exhibit similar binding modes within the substrate-binding cleft; specifically, two hydrophobic groups of the inhibitor interact with +1/+2 tryptophan and a -1 hydrophobic pocket. The structure of the (GlcN) 8 complex surprisingly revealed that the oligosaccharide chain of the inhibitor is orientated in the opposite direction to that previously observed in complexes with other chitinases. Injection of the inhibitors into 4th instar O. furnacalis larvae led to defects in development and pupation. The results of this study provide insights into a general mechanistic principle that confers inhibitory activity against ChtII, which could facilitate rational design of agrochemicals that target ecdysis of insect pests.

  • Organizational Affiliation

    From the State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing 100193, China and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Group II chitinase389Ostrinia furnacalisMutation(s): 0 
Find proteins for A0A221ZS22 (Ostrinia furnacalis)
Explore A0A221ZS22 
Go to UniProtKB:  A0A221ZS22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A221ZS22
Glycosylation Sites: 1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BC0 (Subject of Investigation/LOI)
Query on BC0

Download Ideal Coordinates CCD File 
B [auth A]2-{[(4-chlorophenyl)methyl]sulfanyl}-7-methyl-N-(prop-2-en-1-yl)-7,8-dihydropyrido[4',3':4,5]thieno[2,3-d]pyrimidin-4-amine
C20 H19 Cl N4 S2
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 1.44 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.643α = 90
b = 98.643β = 90
c = 94.884γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31425021

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary