5NRA

Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound 7g


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Targeting Acidic Mammalian chitinase Is Effective in Animal Model of Asthma.

Mazur, M.Olczak, J.Olejniczak, S.Koralewski, R.Czestkowski, W.Jedrzejczak, A.Golab, J.Dzwonek, K.Dymek, B.Sklepkiewicz, P.L.Zagozdzon, A.Noonan, T.Mahboubi, K.Conway, B.Sheeler, R.Beckett, P.Hungerford, W.M.Podjarny, A.Mitschler, A.Cousido-Siah, A.Fadel, F.Golebiowski, A.

(2018) J Med Chem 61: 695-710

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01051
  • Primary Citation of Related Structures:  
    5NR8, 5NRA, 5NRF

  • PubMed Abstract: 

    This article highlights our work toward the identification of a potent, selective, and efficacious acidic mammalian chitinase (AMCase) inhibitor. Rational design, guided by X-ray analysis of several inhibitors bound to human chitotriosidase (hCHIT1), led to the identification of compound 7f as a highly potent AMCase inhibitor (IC 50 values of 14 and 19 nM against human and mouse enzyme, respectively) and selective (>150× against mCHIT1) with very good PK properties. This compound dosed once daily at 30 mg/kg po showed significant anti-inflammatory efficacy in HDM-induced allergic airway inflammation in mice, reducing inflammatory cell influx in the BALF and total IgE concentration in plasma, which correlated with decrease of chitinolytic activity. Therapeutic efficacy of compound 7f in the clinically relevant aeroallergen-induced acute asthma model in mice provides a rationale for developing AMCase inhibitor for the treatment of asthma.


  • Organizational Affiliation

    OncoArendi Therapeutics SA , Żwirki i Wigury 101, 02-089 Warsaw, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitotriosidase-1377Homo 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
PHAROS:  Q13231
GTEx:  ENSG00000133063 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13231
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
95K
Query on 95K

Download Ideal Coordinates CCD File 
B [auth A]1-(5-azanyl-4~{H}-1,2,4-triazol-3-yl)-~{N}-[2-(4-bromophenyl)ethyl]-~{N}-(2-methylpropyl)piperidin-4-amine
C19 H29 Br N6
WDVUKPMRFMWTDG-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
95K Binding MOAD:  5NRA IC50: 123 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.138 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.451α = 90
b = 105.579β = 90
c = 42.137γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 1.2: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description