4MRF

Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fragment-Based Identification of an Inducible Binding Site on Cell Surface Receptor CD44 for the Design of Protein-Carbohydrate Interaction Inhibitors.

Liu, L.K.Finzel, B.C.

(2014) J Med Chem 57: 2714-2725

  • DOI: 10.1021/jm5000276
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Selective inhibitors of hyaluronan (HA) binding to the cell surface receptor CD44 will have value as probes of CD44-mediated signaling and have potential as therapeutic agents in chronic inflammation, cardiovascular disease, and cancer. Using biophys ...

    Selective inhibitors of hyaluronan (HA) binding to the cell surface receptor CD44 will have value as probes of CD44-mediated signaling and have potential as therapeutic agents in chronic inflammation, cardiovascular disease, and cancer. Using biophysical binding assays, fragment screening, and crystallographic characterization of complexes with the CD44 HA binding domain, we have discovered an inducible pocket adjacent to the HA binding groove into which small molecules may bind. Iterations of fragment combination and structure-driven design have allowed identification of a series of 1,2,3,4-tetrahydroisoquinolines as the first nonglycosidic inhibitors of the CD44-HA interaction. The affinity of these molecules for the CD44 HA binding domain parallels their ability to interfere with CD44 binding to polymeric HA in vitro. X-ray crystallographic complexes of lead compounds are described and compared to a new complex with a short HA tetrasaccharide, to establish the tetrahydroisoquinoline pharmacophore as an attractive starting point for lead optimization.


    Related Citations: 
    • Structures of the Cd44-hyaluronan complex provide insight into a fundamental carbohydrate-protein interaction.
      Banerji, S., Wright, A.J., Noble, M., Mahoney, D.J., Campbell, I.D., Day, A.J., Jackson, D.G.
      (2007) Nat Struct Mol Biol 14: 234

    Organizational Affiliation

    Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CD44 antigen
A
150Mus musculusMutation(s): 0 
Gene Names: Cd44Cd44 Ly-24Ly-24
Find proteins for P15379 (Mus musculus)
Go to UniProtKB:  P15379
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2CK
Query on 2CK

Download CCD File 
A
1,2,3,4-tetrahydroisoquinoline
C9 H11 N
UWYZHKAOTLEWKK-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2CKKd:  11200000   nM  Binding MOAD
2CKIC50:  27000000   nM  BindingDB
2CKKd:  11200000   nM  BindingDB
2CKKd:  6900000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.805α = 90
b = 81.626β = 118.28
c = 32.358γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-09-17 
  • Released Date: 2014-04-16 
  • Deposition Author(s): Liu, L.K., Finzel, B.

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection