6JKF

Crystal structure of Serratia marcescens Chitinase B complexed with compound 2-8-s2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors.

Jiang, X., Kumar, A., Motomura, Y., Liu, T., Zhou, Y., Moro, K., Zhang, K.Y.J., Yang, Q.

(2020) J Med Chem 63: 987-1001

  • DOI: 10.1021/acs.jmedchem.9b01154
  • Primary Citation of Related Structures:  
    6JJR, 6JK6, 6JKF, 6JK9, 6JMN

  • PubMed Abstract: 

    • Chitinases not only play vital roles in the human innate immune system but are also essential for the development of pathogenic fungi and pests. Chitinase inhibitors are efficient tools to investigate the elusive role of human chitinases and to control pathogens and pests ...

    Chitinases not only play vital roles in the human innate immune system but are also essential for the development of pathogenic fungi and pests. Chitinase inhibitors are efficient tools to investigate the elusive role of human chitinases and to control pathogens and pests. Via hierarchical virtual screening, we have discovered a series of chitinase inhibitors with a novel scaffold that have high inhibitory activities and selectivities against human and insect chitinases. The most potent human chitotriosidase inhibitor, compound 40 , exhibited a K i of 49 nM, and the most potent inhibitor of the insect pest chitinase Of Chi-h, compound 53 , exhibited a K i of 9 nM. The binding of these two most potent inhibitors was confirmed by X-ray crystallography. In a murine model of bleomycin-induced pulmonary fibrosis, compound 40 was found to suppress the chitotriosidase activity by 60%, leading to a significant increase in inflammatory cells and suggesting that chitotriosidase played a protective role.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chitinase A, B497Serratia marcescensMutation(s): 0 
Gene Names: chiB
EC: 3.2.1.14
Find proteins for P11797 (Serratia marcescens)
Explore P11797 
Go to UniProtKB:  P11797
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BV0
Query on BV0
Download Ideal Coordinates CCD File 
A, B
6-azanyl-11-methyl-2-oxidanylidene-7-[[(2R)-oxolan-2-yl]methyl]-N-(pyridin-3-ylmethyl)-1,9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-3(8),4,6,9,11,13-hexaene-5-carboxamide
C24 H25 N6 O3
XPXWHWPEIBBBCJ-QGZVFWFLSA-O		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.767α = 90
b = 104.997β = 90
c = 185.868γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-02-28 
  • Released Date: 2020-02-19 
    • Deposition Author(s): Yang, Q., Jiang, X.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31425021

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references