Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Ligand Interaction

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

 3D View: Structure | Ligand Interaction

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 88.59 kDa 
• Atom Count: 6052 
• Residue Count: 736 
• Unique protein chains: 1

1RD4

An allosteric inhibitor of LFA-1 bound to its I-domain

• DOI: 10.2210/pdb1RD4/pdb

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


• Deposited: 2003-11-05 Released: 2004-03-30 
• Deposition Author(s): Crump, M.P., Ceska, T.A., Spyracopoulos, L., Henry, A., Archibald, S.C., Alexander, R., Taylor, R.J., Findlow, S.C., O'Connell, J., Robinson, M.K., Shock, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.290 
• R-Value Work: 0.236 
• R-Value Observed: 0.245 

Literature

Structure of an allosteric inhibitor of LFA-1 bound to the I-domain studied by crystallography, NMR, and calorimetry

Crump, M.P., Ceska, T.A., Spyracopoulos, L., Henry, A., Archibald, S.C., Alexander, R., Taylor, R.J., Findlow, S.C., O'Connell, J., Robinson, M.K., Shock, A.

(2004) Biochemistry 43: 2394-2404

• PubMed: 14992576 
• DOI: 10.1021/bi035422a
• Primary Citation of Related Structures:  
  1RD4


• PubMed Abstract: 
  

LFA-1 (lymphocyte function-associated antigen-1) plays a role in intercellular adhesion and lymphocyte trafficking and activation and is an attractive anti-inflammatory drug target. The alpha-subunit of LFA-1, in common with several other integrins, has an N-terminally inserted domain (I-domain) of approximately 200 amino acids that plays a central role in regulating ligand binding to LFA-1. An additional region, termed the I-domain allosteric site (IDAS), has been identified exclusively within the LFA-1 I-domain and shown to regulate the function of this protein. The IDAS is occupied by small molecule LFA-1 inhibitors when cocrystallized or analyzed by (15)N-(1)H HSQC (heteronuclear single-quantum coherence) NMR (nuclear magnetic resonance) titration experiments. We report here a novel arylthio inhibitor that binds the I-domain with a K(d) of 18.3 nM as determined by isothermal titration calorimetry (ITC). This value is in close agreement with the IC(50) (10.9 nM) derived from a biochemical competition assay (DELFIA) that measures the level of inhibition of binding of whole LFA-1 to its ligand, ICAM-1. Having established the strong affinity of the arylthio inhibitor for the isolated I-domain, we have used a range of techniques to further characterize the binding, including ITC, NMR, and X-ray crystallography. We have first developed an effective ITC binding assay for use with low-solubility inhibitors that avoids the need for ELISA-based assays. In addition, we utilized a fast NMR-based assay for the generation of I-domain-inhibitor models. This is based around the collection of HCCH-TOCSY spectra of LFA-1 in the bound form and the identification of a subset of side chain methyl groups that give chemical shift changes upon binding of LFA-1 inhibitors. This subset was used in two-dimensional (13)C-(15)N and (15)N-filtered and -edited two-dimensional NMR experiments to identify a minimal set of intraligand and ligand-protein NOEs, respectively (nuclear Overhauser enhancements). Models from the NMR data were assessed by comparison to an X-ray crystallographic structure of the complex, confirming that the method correctly predicted the essential features of the bound ligand.

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Organizational Affiliation: 

School of Biological Sciences, University of Southampton, Bassett Crescent East, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-L	A, B, C, D	191	Homo sapiens	Mutation(s): 0  Gene Names: ITGAL, CD11A
Find proteins for P20701 (Homo sapiens) Explore P20701  Go to UniProtKB:  P20701
NIH Common Fund Data Resources
PHAROS  P20701 GTEx  ENSG00000005844

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L08	A, B, C, D	1-ACETYL-4-(4-{4-[(2-ETHOXYPHENYL)THIO]-3-NITROPHENYL}PYRIDIN-2-YL)PIPERAZINE C25 H26 N4 O4 S GKGJFUXSTSUKPB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
L08	Kd :  18.299999237060547   nM  PDBBind
L08	Kd:  18.299999237060547   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.290 
• R-Value Work: 0.236 
• R-Value Observed: 0.245 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.96	α = 74.21
b = 64.41	β = 90
c = 66.21	γ = 87.26

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-05 
• Released Date: 2004-03-30 
Deposition Author(s): Crump, M.P., Ceska, T.A., Spyracopoulos, L., Henry, A., Archibald, S.C., Alexander, R., Taylor, R.J., Findlow, S.C., O'Connell, J., Robinson, M.K., Shock, A.

Revision History 

• Version 1.0: 2004-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection