1XDG

X-ray structure of LFA-1 I-domain in complex with LFA878 at 2.1A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Improved lymphocyte function-associated antigen-1 (LFA-1) inhibition by statin derivatives: molecular basis determined by x-ray analysis and monitoring of LFA-1 conformational changes in vitro and ex vivo

Weitz-Schmidt, G.Welzenbach, K.Dawson, J.Kallen, J.

(2004) J.Biol.Chem. 279: 46764-46771

  • DOI: 10.1074/jbc.M407951200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The integrin lymphocyte function-associated antigen-1 (LFA-1) (alphaLbeta2; CD11a/CD18) plays an important role in leukocyte migration and T cell activation. LFA-1 is inhibited by the cholesterol-lowering drug lovastatin, which binds to an allosteric ...

    The integrin lymphocyte function-associated antigen-1 (LFA-1) (alphaLbeta2; CD11a/CD18) plays an important role in leukocyte migration and T cell activation. LFA-1 is inhibited by the cholesterol-lowering drug lovastatin, which binds to an allosteric site of the alphaL I domain termed the lovastatin site (L-site). Here we report for the first time the x-ray structures of the LFA-1 I domain complexed with derivatives of lovastatin optimized for LFA-1 inhibition. This analysis identified two new subpockets within the L-site occupied by chemical groups of the statin derivatives but not by lovastatin itself. Occupancy of these L-site subpockets led to distinct conformational changes in LFA-1, which were detectable by an epitope-monitoring assay. We utilized this assay to demonstrate improved LFA-1 inhibition in human blood in vitro and in blood samples from treated animals ex vivo. Moreover, we demonstrate that the novel lovastatin-derived LFA-1 inhibitor LFA878 exhibits potent anti-inflammatory effects in carrageenan-induced rat paw edema. In summary, the findings reported here extend the understanding of LFA-1 inhibition at the molecular level, allow for the identification and design of LFA-1 inhibitors of further enhanced potency, and support the expectation that LFA-1 inhibitors binding to the L-site will be of therapeutic value in treating inflammatory diseases.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-L
A, B
188Homo sapiensMutation(s): 0 
Gene Names: ITGAL (CD11A)
Find proteins for P20701 (Homo sapiens)
Go to Gene View: ITGAL
Go to UniProtKB:  P20701
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AB8
Query on AB8

Download SDF File 
Download CCD File 
A, B
(1S,3R,8AS)-8-(2-{(4S,6S)-3-(4-HYDROXY-3-METHOXYBENZYL)-4-[2-(METHYLAMINO)-2-OXOETHYL]-2-OXO-1,3-OXAZINAN-6-YL}ETHYL)-3,7-DIMETHYL-1,2,3,7,8,8A-HEXAHYDRONAPHTHALEN-1-YL (2R)-2-METHYLBUTANOATE
LFA878; (S)-2-METHYL-BUTYRIC ACID (1S,3R,7S,8S,8AR)-8-{2-[(4R,6R)-3-(4-HYDROXY-3-METHOXY-BENZYL)-4-METHYLCARBAMOYLMETHYL-2-OXO-[1,3]OXAZINAN-6-YL]-ETHYL}-3,7-DIMETHYL-1,2,3,7,8,8A-HEXAHYDRO-NAPHTHALEN-1-YL ESTER
C34 H48 N2 O7
XGCZRGJUCNQVCO-XFAJEYMZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AB8IC50: 50 nM BINDINGMOAD
AB8IC50: 50 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.900α = 90.00
b = 77.400β = 90.00
c = 92.300γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-02-20
    Type: Database references