8Z1S | pdb_00008z1s

Crystal structure of mouse Galectin-3 in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.276 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Atropisomerism Observed in Galactose-Based Monosaccharide Inhibitors of Galectin-3 Comprising 2-Methyl-4-phenyl-2,4-dihydro-3 H -1,2,4-triazole-3-thione.

Yoon, D.S.Liu, C.Jalagam, P.R.Feng, J.Wang, W.Swidorski, J.J.Xu, L.Hartz, R.A.Nair, S.K.Beno, B.R.Panda, M.Ghosh, K.Kumar, A.Sale, H.Shah, D.Mathur, A.Ellsworth, B.A.Cheng, D.Regueiro-Ren, A.

(2024) J Med Chem 67: 14184-14199

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01008
  • Primary Citation of Related Structures:  
    8Z1S, 8Z1T, 8Z25, 8ZUV

  • PubMed Abstract: 

    Galectin-3 (Gal-3) is a carbohydrate binding protein that has been implicated in the development and progression of fibrotic diseases. Proof-of-principal animal models have demonstrated that inhibition of Gal-3 is a potentially viable pathway for the treatment of fibrosis─with small molecule Gal-3 inhibitors advanced into clinical trials. We hereby report the discovery of novel galactose-based monosaccharide Gal-3 inhibitors comprising 2-methyl-4-phenyl-2,4-dihydro-3 H -1,2,4-triazole-3-thione (compound 20 ) and 4-phenyl-4 H -1,2,4-triazole (compound 15 ). Notably, hindered rotation caused by steric interaction between the 3-thione and ortho -trifluoromethyl group of compounds 20 , 21 induced formation of thermodynamically stable atropisomers. Distinct X-ray cocrystal structures of 20 and 21 were obtained, which clearly demonstrated that the configuration of 21 proscribes a key halogen bonding σ-hole interaction of 3-chloro with carbonyl oxygen of Gly182, thereby leading to significant loss in potency. Ultimately, 20 and 15 were evaluated in mouse pharmacokinetic studies, and both compounds exhibited oral exposures suitable for further in vivo assessment.


  • Organizational Affiliation

    Research and Early Development, Bristol Myers Squibb, P.O. Box 5400, Princeton, New Jersey 08543-5400, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3
A, B
179Homo sapiensMutation(s): 2 
Gene Names: LGALS3MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens)
Explore P17931 
Go to UniProtKB:  P17931
PHAROS:  P17931
GTEx:  ENSG00000131981 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17931
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L0Q (Subject of Investigation/LOI)
Query on A1L0Q

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
(2~{S},3~{R},4~{R},5~{R},6~{R})-4-[4-[4-chloranyl-3,5-bis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-2-[4-[5-chloranyl-2-(trifluoromethyl)phenyl]-5-methyl-1,2,4-triazol-3-yl]-6-(hydroxymethyl)oxane-3,5-diol
C24 H19 Cl2 F5 N6 O4
JRURYEFDCGQBFQ-WHCFWRGISA-N
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.276 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.614α = 90
b = 64.997β = 90
c = 74.607γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1L0QClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release