6ZE8

Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound OATD-01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of OATD-01 , a First-in-Class Chitinase Inhibitor as Potential New Therapeutics for Idiopathic Pulmonary Fibrosis.

Koralewski, R.Dymek, B.Mazur, M.Sklepkiewicz, P.Olejniczak, S.Czestkowski, W.Matyszewski, K.Andryianau, G.Niedziejko, P.Kowalski, M.Gruza, M.Borek, B.Jedrzejczak, K.Bartoszewicz, A.Pluta, E.Rymaszewska, A.Kania, M.Rejczak, T.Piasecka, S.Mlacki, M.Mazurkiewicz, M.Piotrowicz, M.Salamon, M.Zagozdzon, A.Napiorkowska-Gromadzka, A.Bartlomiejczak, A.Mozga, W.Dobrzanski, P.Dzwonek, K.Golab, J.Nowotny, M.Olczak, J.Golebiowski, A.

(2020) J Med Chem 63: 15527-15540

  • DOI: 10.1021/acs.jmedchem.0c01179
  • Primary Citation of Related Structures:  
    6ZE8

  • PubMed Abstract: 
  • Chitotriosidase (CHIT1) and acidic mammalian chitinase (AMCase) are the enzymatically active chitinases that have been implicated in the pathology of chronic lung diseases such as asthma and interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF) and sarcoidosis ...

    Chitotriosidase (CHIT1) and acidic mammalian chitinase (AMCase) are the enzymatically active chitinases that have been implicated in the pathology of chronic lung diseases such as asthma and interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF) and sarcoidosis. The clinical and preclinical data suggest that pharmacological inhibition of CHIT1 might represent a novel therapeutic approach in IPF. Structural modification of an advanced lead molecule 3 led to the identification of compound 9 ( OATD-01) , a highly active CHIT1 inhibitor with both an excellent PK profile in multiple species and selectivity against a panel of other off-targets. OATD-01 given orally once daily in a range of doses between 30 and 100 mg/kg showed significant antifibrotic efficacy in an animal model of bleomycin-induced pulmonary fibrosis. OATD-01 is the first-in-class CHIT1 inhibitor, currently completed phase 1b of clinical trials, to be a potential treatment for IPF.


    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
MoleculeChainsSequence LengthOrganismDetailsImage
Chitotriosidase-1
A, B, C, D, E, F
A, B, C, D, E, F
365Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QGB (Subject of Investigation/LOI)
Query on QGB

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D],
P [auth E],
G [auth A],
I [auth B],
K [auth C],
M [auth D],
P [auth E],
R [auth F]
5-(4-((2S,5S)-5-(4-chlorobenzyl)-2-methylmorpholino)piperidin-1-yl)-4H-1,2,4-triazol-3-amine
C19 H27 Cl N6 O
STWVLEKJQQRGMO-GUYCJALGSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
N [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
L [auth C],
O [auth D],
Q [auth E],
H [auth A],
J [auth B],
L [auth C],
O [auth D],
Q [auth E],
S [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
QGB Binding MOAD:  6ZE8 IC50: 23 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.325α = 90
b = 93.744β = 90
c = 281.642γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHELXSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2021-01-06
    Changes: Database references