9FXZ | pdb_00009fxz

Galectin-8 N-terminal carbohydrate recognition domain in complex with 4-(bromophenyl)phthalazinone D-galactal ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.157 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Galectin-8N-Selective 4-Halophenylphthalazinone-Galactals Double pi-Stack in a Unique Pocket.

van Klaveren, S.Hassan, M.Hakansson, M.Johnsson, R.E.Larsson, J.Jakopin, Z.Anderluh, M.Leffler, H.Tomasic, T.Nilsson, U.J.

(2024) ACS Med Chem Lett 15: 1319-1324

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00212
  • Primary Citation of Related Structures:  
    9FXZ

  • PubMed Abstract: 

    Galectin-8 contains two different carbohydrate recognition domains (CRDs). Selective inhibitors for at least one CRD are desirable for galectin-8 biology studies and potentially for pharmacological purposes. Structure-guided design led to the discovery of potent and selective glycomimetic-heterocycle hybrid ligands, with a 4-( p -bromophenyl)phthalazinone derivative displaying a 34 μM K d for galectin-8N (N-terminal CRD), no binding to galectin-8C (C-terminal CRD), -1, -3, -4N, -7, -9C, or -9N, and >40-fold selectivity over galectin-4C. Selectivity was achieved with the halogenated 4-phenylphthalazinone moiety occupying a galectin-8N-specific sub-pocket. A 1.30 Å resolution X-ray structure revealed the phthalazinone moiety stacking with Arg45 and the 4-bromophenyl moiety stacking both Arg59 and Tyr141 of galectin-8N. Physicochemical and in vitro ADME studies revealed a desirable LogD, which also translated to good passive permeability. The chemical, microsome, and plasma stability support these compounds as promising tool compounds and candidates for hit-to-lead optimization.


  • Organizational Affiliation
    • Department of Chemistry, Faculty of Science, Lund University, Naturvetarvägen 14, 223 62, Lund, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-8
A, B
317Homo sapiensMutation(s): 0 
Gene Names: LGALS8
UniProt & NIH Common Fund Data Resources
Find proteins for O00214 (Homo sapiens)
Explore O00214 
Go to UniProtKB:  O00214
PHAROS:  O00214
GTEx:  ENSG00000116977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00214
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.157 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.71α = 90
b = 62.28β = 90
c = 84.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union765581

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release