3E2M

LFA-1 I domain bound to inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-activity relationship of ortho- and meta-phenol based LFA-1 ICAM inhibitors

Lin, E.Y.Guckian, K.M.Silvian, L.Chin, D.Boriack-Sjodin, P.A.van Vlijmen, H.Friedman, J.E.Scott, D.M.

(2008) Bioorg Med Chem Lett 18: 5245-5248

  • DOI: https://doi.org/10.1016/j.bmcl.2008.08.062
  • Primary Citation of Related Structures:  
    3BQN, 3E2M

  • PubMed Abstract: 

    LFA-1 ICAM inhibitors based on ortho- and meta-phenol templates were designed and synthesized by Mitsunobu chemistry. The selection of targets was guided by X-ray co-crystal data, and led to compounds which showed an up to 30-fold increase in potency over reference compound 1 in the LFA-1/ICAM1-Ig assay. The most active compound exploited a new hydrogen bond to the I-domain and exhibited subnanomolar potency.


  • Organizational Affiliation

    Research and Development, Biogen Idec Inc., 14 Cambridge Center, Cambridge, MA 02142, USA. ted.lin@biogenidec.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-L
A, B
185Homo sapiensMutation(s): 1 
Gene Names: ITGALCD11A
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens)
Explore P20701 
Go to UniProtKB:  P20701
PHAROS:  P20701
GTEx:  ENSG00000005844 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20701
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E2M
Query on E2M

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
cis-4-{[2-({4-[(1E)-3-morpholin-4-yl-3-oxoprop-1-en-1-yl]-2,3-bis(trifluoromethyl)phenyl}sulfanyl)phenoxy]methyl}cyclohexanecarboxylic acid
C29 H29 F6 N O5 S
AXSOGTWJBSDWJQ-WZEPYWGYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
E2M PDBBind:  3E2M IC50: 0.4 (nM) from 1 assay(s)
BindingDB:  3E2M IC50: 0.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.062α = 90
b = 69.608β = 90
c = 72.363γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description