6JK6

Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound 2-8-s2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.9b01154
  • Primary Citation of Related Structures:  
    6JJR, 6JK6, 6JK9, 6JKF, 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. 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

    School of Bioengineering , Dalian University of Technology , 2 Linggong Road , Dalian 116024 , China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitotriosidase-1381Homo sapiensMutation(s): 0 
Gene Names: CHIT1
EC: 3.2.1.14
UniProt & NIH Common Fund Data Resources
Find proteins for Q13231 (Homo sapiens)
Explore Q13231 
Go to UniProtKB:  Q13231
GTEx:  ENSG00000133063 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13231
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BV0
Query on BV0

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.726α = 90
b = 66.726β = 90
c = 88.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description