7XFA

Structure of human Galectin-3 CRD in complex with monosaccharide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of Monosaccharide Derivatives as Potent, Selective, and Orally Bioavailable Inhibitors of Human and Mouse Galectin-3.

Liu, C.Jalagam, P.R.Feng, J.Wang, W.Raja, T.Sura, M.R.Manepalli, R.K.V.L.P.Aliphedi, B.R.Medavarapu, S.Nair, S.K.Muthalagu, V.Natesan, R.Gupta, A.Beno, B.Panda, M.Ghosh, K.Shukla, J.K.Sale, H.Haldar, P.Kalidindi, N.Shah, D.Patel, D.Mathur, A.Ellsworth, B.A.Cheng, D.Regueiro-Ren, A.

(2022) J Med Chem 65: 11084-11099

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00517
  • Primary Citation of Related Structures:  
    7XFA

  • PubMed Abstract: 

    Galectin-3 (Gal-3), a member of the β-galactoside-binding protein family, is implicated in a wide variety of human diseases. Identification of Gal-3 inhibitors with the right combination of potency (against both human and mouse Gal-3) and pharmacokinetic properties to fully evaluate the potential of Gal-3 for therapeutic intervention has been a major challenge due to the characteristics of its binding pocket: high hydrophilicity and key structural differences between human Gal-3 and the mouse ortholog. We report the discovery of a novel series of monosaccharide-based, highly potent, and orally bioavailable inhibitors of human and mouse Gal-3. The novel monosaccharide derivatives proved to be selective for Gal-3, the only member of the chimeric type of galectins, over Gal-1 and Gal-9, representative of the prototype and tandem-repeat type of galectins, respectively. The proposed binding mode for the newly identified ligands was confirmed by an X-ray cocrystal structure of a representative analogue bound to Gal-3 protein.


  • Organizational Affiliation

    Department of Small Molecule Drug Discovery, Research & Early Development, Bristol Myers Squibb Company, Princeton, New Jersey 08543, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-3165Homo sapiensMutation(s): 0 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D9J (Subject of Investigation/LOI)
Query on D9J

Download Ideal Coordinates CCD File 
B [auth A](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-[2-[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
OBZWBMTWYDLHBX-WHCFWRGISA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.98 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.824α = 90
b = 58.187β = 90
c = 63.118γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description