5NR8 | pdb_00005nr8

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

PDB DOI: https://doi.org/10.2210/pdb5NR8/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-04-22 Released: 2018-02-21
Deposition Author(s): Podjarny, A., Fadel, F., Golebiowski, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.168 (DCC)
R-Value Work:
0.145 (DCC)

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

PubMed: 29283260 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.7b01051
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 43.16 kDa
Atom Count: 3,440
Modeled Residue Count: 377
Deposited Residue Count: 377
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitotriosidase-1	A	377	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13231
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
95N Query on 95N Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-(3-azanyl-1~{H}-1,2,4-triazol-5-yl)-~{N}-[2-(4-bromophenyl)ethyl]-~{N}-methyl-piperidin-4-amine C₁₆ H₂₃ Br N₆ DRIHQKATVUWZLY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
95N	BindingDB: 5NR8	IC50: 175 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.168 (DCC)
R-Value Work: 0.145 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.897	α = 90
b = 106.006	β = 90
c = 42.158	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-02-21

Deposition Author(s):

Podjarny, A.

Fadel, F.

Golebiowski, A.

Revision History (Full details and data files)

Version 1.0: 2018-02-21
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-10-23
Changes: Data collection, Database references, Structure summary