3E2M

LFA-1 I domain bound to inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.287 (Depositor) 
  • R-Value Work: 
    0.215 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted E2MClick on this verticalbar to view details

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 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 (Depositor) 
  • R-Value Work:  0.215 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted E2MClick on this verticalbar to view details

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