Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.11 kDa 
• Atom Count: 3335 
• Modelled Residue Count: 364 
• Deposited Residue Count: 376 
• Unique protein chains: 1

1XDD

X-ray structure of LFA-1 I-domain in complex with LFA703 at 2.2A resolution

• PDB DOI: 10.2210/pdb1XDD/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-06 Released: 2004-09-21 
• Deposition Author(s): Weitz-Schmidt, G., Welzenbach, K., Dawson, J., Kallen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.206 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 

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

• PubMed: 15304496 
• DOI: 10.1074/jbc.M407951200
• Primary Citation of Related Structures:  
  1XDD, 1XDG


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-L	A, B	188	Homo sapiens	Mutation(s): 0  Gene Names: ITGAL, CD11A
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens) Explore P20701  Go to UniProtKB:  P20701
PHAROS:  P20701

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AAY	D [auth A], F [auth B]	8-[2-((2S)-4-HYDROXY-1-{[5-(HYDROXYMETHYL)-6-METHOXY-2-NAPHTHYL]METHYL}-6-OXOPIPERIDIN-2-YL)ETHYL]-3,7-DIMETHYL-1,2,3,7,8,8A-HEXAHYDRONAPHTHALEN-1-YL 2-METHYLBUTANOATE C37 H49 N O6 WPVRNXUYVXQXPY-YFAYRSKXSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AAY	Binding MOAD:  1XDD	IC50: 200 (nM) from 1 assay(s)
	PDBBind:  1XDD	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.206 
• R-Value Work: 0.161 
• R-Value Observed: 0.164 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.7	α = 90
b = 116.7	β = 90
c = 82.8	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-06 
• Released Date: 2004-09-21 
Deposition Author(s): Weitz-Schmidt, G., Welzenbach, K., Dawson, J., Kallen, J.

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-02-20
  Changes: Database references
• Version 1.4: 2014-11-12
  Changes: Structure summary