8R42

Structure of CHI3L1 in complex with inhibititor 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1.

Czestkowski, W.Krzeminski, L.Piotrowicz, M.C.Mazur, M.Pluta, E.Andryianau, G.Koralewski, R.Matyszewski, K.Olejniczak, S.Kowalski, M.Lisiecka, K.Koziel, R.Piwowar, K.Papiernik, D.Nowotny, M.Napiorkowska-Gromadzka, A.Nowak, E.Niedzialek, D.Wieczorek, G.Siwinska, A.Rejczak, T.Jedrzejczak, K.Mulewski, K.Olczak, J.Zaslona, Z.Golebiowski, A.Drzewicka, K.Bartoszewicz, A.

(2024) J Med Chem 67: 3959-3985

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02255
  • Primary Citation of Related Structures:  
    8R41, 8R42, 8R4X

  • PubMed Abstract: 

    Chitinase-3-like-1 (CHI3L1), also known as YKL-40, is a glycoprotein linked to inflammation, fibrosis, and cancer. This study explored CHI3L1's interactions with various oligosaccharides using microscale thermophoresis (MST) and AlphaScreen (AS). These investigations guided the development of high-throughput screening assays to assess interference of small molecules in binding between CHI3L1 and biotinylated small molecules or heparan sulfate-based probes. Small molecule binders of YKL-40 were identified in our chitotriosidase inhibitors library with MST and confirmed through X-ray crystallography. Based on cocrystal structures of potent hit compounds with CHI3L1, small molecule probes 19 and 20 were designed for an AS assay. Structure-based optimization led to compounds 30 and 31 with nanomolar activities and drug-like properties. Additionally, an orthogonal AS assay using biotinylated heparan sulfate as a probe was developed. The compounds' affinity showed a significant correlation in both assays. These screening tools and compounds offer novel avenues for investigating the role of CHI3L1.


  • Organizational Affiliation

    Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase-3-like protein 1
A, B
383Homo sapiensMutation(s): 0 
Gene Names: CHI3L1
UniProt & NIH Common Fund Data Resources
Find proteins for P36222 (Homo sapiens)
Explore P36222 
Go to UniProtKB:  P36222
PHAROS:  P36222
GTEx:  ENSG00000133048 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36222
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P36222-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth X],
D [auth Y]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XUC (Subject of Investigation/LOI)
Query on XUC

Download Ideal Coordinates CCD File 
E [auth A],
Q [auth B]
2-[4-[(2~{R})-2-[(4-chlorophenyl)methyl]pyrrolidin-1-yl]piperidin-1-yl]pyridine
C21 H26 Cl N3
XCVVDQHGTQAUAD-HXUWFJFHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
O [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
P [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.48α = 90
b = 121.89β = 90
c = 136.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted XUCClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Structure summary