5H9S

Crystal Structure of Human Galectin-7 in Complex with TAZTDG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Dual thio-digalactoside-binding modes of human galectins as the structural basis for the design of potent and selective inhibitors

Hsieh, T.J.Lin, H.Y.Tu, Z.Lin, T.C.Wu, S.C.Tseng, Y.Y.Liu, F.T.Danny Hsu, S.T.Lin, C.H.

(2016) Sci Rep 6: 29457-29457

  • DOI: https://doi.org/10.1038/srep29457
  • Primary Citation of Related Structures:  
    4Y24, 5H9P, 5H9Q, 5H9R, 5H9S

  • PubMed Abstract: 

    Human galectins are promising targets for cancer immunotherapeutic and fibrotic disease-related drugs. We report herein the binding interactions of three thio-digalactosides (TDGs) including TDG itself, TD139 (3,3'-deoxy-3,3'-bis-(4-[m-fluorophenyl]-1H-1,2,3-triazol-1-yl)-thio-digalactoside, recently approved for the treatment of idiopathic pulmonary fibrosis), and TAZTDG (3-deoxy-3-(4-[m-fluorophenyl]-1H-1,2,3-triazol-1-yl)-thio-digalactoside) with human galectins-1, -3 and -7 as assessed by X-ray crystallography, isothermal titration calorimetry and NMR spectroscopy. Five binding subsites (A-E) make up the carbohydrate-recognition domains of these galectins. We identified novel interactions between an arginine within subsite E of the galectins and an arene group in the ligands. In addition to the interactions contributed by the galactosyl sugar residues bound at subsites C and D, the fluorophenyl group of TAZTDG preferentially bound to subsite B in galectin-3, whereas the same group favored binding at subsite E in galectins-1 and -7. The characterised dual binding modes demonstrate how binding potency, reported as decreased Kd values of the TDG inhibitors from μM to nM, is improved and also offer insights to development of selective inhibitors for individual galectins.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin-7
A, B
155Homo sapiensMutation(s): 0 
Gene Names: LGALS7PIG1LGALS7B
UniProt & NIH Common Fund Data Resources
Find proteins for P47929 (Homo sapiens)
Explore P47929 
Go to UniProtKB:  P47929
PHAROS:  P47929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47929
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TGZ
Query on TGZ

Download Ideal Coordinates CCD File 
C [auth B](2~{S},3~{R},4~{S},5~{R},6~{R})-2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-4-[4-(3-fluorophenyl)-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]sulfanyl-6-(hydroxymethyl)oxane-3,4,5-triol
C20 H26 F N3 O9 S
PZQVUALSHLQTOK-UYIOFKAJSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TGZ Binding MOAD:  5H9S Kd: 8.70e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.873α = 90
b = 64.475β = 90
c = 73.046γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia SinicaTaiwan--
Ministry of Science and TechnologyTaiwan102-2113-M-001-001-MY3
Ministry of Science and TechnologyTaiwan102-2923-M-001-001-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description