6QLQ

Galectin-3C in complex with fluoroaryltriazole monothiogalactoside derivative 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure and Energetics of Ligand-Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides: Insight into Solvation Effects and Multipolar Interactions.

Kumar, R.Ignjatovic, M.M.Peterson, K.Olsson, M.Leffler, H.Ryde, U.Nilsson, U.J.Logan, D.T.

(2019) ChemMedChem 14: 1528-1536

  • DOI: 10.1002/cmdc.201900293
  • Primary Citation of Related Structures:  
    6QLN, 6QLO, 6QLP, 6QLQ, 6QLR, 6QLS, 6QLT, 6QLU

  • PubMed Abstract: 
  • Multipolar fluorine-amide interactions with backbone and side-chain amides have been described as important for protein-ligand interactions and have been used to improve the potency of synthetic inhibitors. In this study, fluorine interactions within a well-defined binding pocket on galectin-3 were investigated systematically using phenyltriazolyl-thiogalactosides fluorinated singly or multiply at various positions on the phenyl ring ...

    Multipolar fluorine-amide interactions with backbone and side-chain amides have been described as important for protein-ligand interactions and have been used to improve the potency of synthetic inhibitors. In this study, fluorine interactions within a well-defined binding pocket on galectin-3 were investigated systematically using phenyltriazolyl-thiogalactosides fluorinated singly or multiply at various positions on the phenyl ring. X-ray structures of the C-terminal domain of galectin-3 in complex with eight of these ligands revealed potential orthogonal fluorine-amide interactions with backbone amides and one with a side-chain amide. The two interactions involving main-chain amides seem to have a strong influence on affinity as determined by fluorescence anisotropy. In contrast, the interaction with the side-chain amide did not influence affinity. Quantum mechanics calculations were used to analyze the relative contributions of these interactions to the binding energies. No clear correlation could be found between the relative energies of the fluorine-main-chain amide interactions and the overall binding energy. Instead, dispersion and desolvation effects play a larger role. The results confirm that the contribution of fluorine-amide interactions to protein-ligand interactions cannot simply be predicted, on geometrical considerations alone, but require careful consideration of the energetic components.


    Organizational Affiliation

    Department of Chemistry, Division of Biochemistry & Structural Biology, Lund University, Box 124, 22100, Lund, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galectin-3A [auth B]138Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17931
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J4E (Subject of Investigation/LOI)
Query on J4E

Download Ideal Coordinates CCD File 
C [auth B](2~{R},3~{R},4~{S},5~{R},6~{S})-4-[4-(4-fluorophenyl)-1,2,3-triazol-1-yl]-2-(hydroxymethyl)-6-(4-methylphenyl)sulfanyl-oxane-3,5-diol
C21 H22 F N3 O4 S
LEJGTTBPRKJROI-IFLJBQAJSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
B DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
J4E Binding MOAD:  6QLQ Kd: 3.10e+4 (nM) from 1 assay(s)
BindingDB:  6QLQ Kd: 3.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.12α = 90
b = 57.486β = 90
c = 62.668γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSwedenKAW 2013.0022

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references