7DF5 | pdb_00007df5

Human Galectin-3 CRD in complex with novel tetrahydropyran-based thiodisaccharide mimic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 
    0.169 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.139 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.141 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H5OClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Synthesis, Structure-Activity Relationships, and In Vivo Evaluation of Novel Tetrahydropyran-Based Thiodisaccharide Mimics as Galectin-3 Inhibitors.

Xu, L.Hartz, R.A.Beno, B.R.Ghosh, K.Shukla, J.K.Kumar, A.Patel, D.Kalidindi, N.Lemos, N.Gautam, S.S.Kumar, A.Ellsworth, B.A.Shah, D.Sale, H.Cheng, D.Regueiro-Ren, A.

(2021) J Med Chem 64: 6634-6655

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02001
  • Primary Citation of Related Structures:  
    7DF5, 7DF6

  • PubMed Abstract: 

    Galectin-3 is a member of a family of β-galactoside-binding proteins. A substantial body of literature reports that galectin-3 plays important roles in cancer, inflammation, and fibrosis. Small-molecule galectin-3 inhibitors, which are generally lactose or galactose-based derivatives, have the potential to be valuable disease-modifying agents. In our efforts to identify novel galectin-3 disaccharide mimics to improve drug-like properties, we found that one of the monosaccharide subunits can be replaced with a suitably functionalized tetrahydropyran ring. Optimization of the structure-activity relationships around the tetrahydropyran-based scaffold led to the discovery of potent galectin-3 inhibitors. Compounds 36 , 40 , and 45 were selected for further in vivo evaluation. The synthesis, structure-activity relationships, and in vivo evaluation of novel tetrahydropyran-based galectin-3 inhibitors are described.


  • Organizational Affiliation

    Department of Small Molecule Drug Discovery, Bristol Myers Squibb Company, Research and Development, P.O. Box 5400, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H5O (Subject of Investigation/LOI)
Query on H5O

Download Ideal Coordinates CCD File 
G [auth A](2R,3R,4S,5R,6S)-2-(hydroxymethyl)-5-methoxy-6-[(3R,4R,5S)-4-oxidanyl-5-(4-pyrimidin-5-yl-1,2,3-triazol-1-yl)oxan-3-yl]sulfanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-3-ol
C26 H27 F3 N8 O6 S
XUWUKOCAMCFANQ-COQUQQDQSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
H5O BindingDB:  7DF5 IC50: min: 19, max: 1250 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free:  0.169 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.139 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.21α = 90
b = 57.34β = 90
c = 62.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata 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 H5OClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description