3BQM | pdb_00003bqm

LFA-1 I domain bound to inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3BQM/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-12-20 Released: 2008-08-19 
• Deposition Author(s): Silvian, L.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

Design and synthesis of a series of meta aniline-based LFA-1 ICAM inhibitors

Guckian, K.M., Lin, E.Y., Silvian, L., Friedman, J.E., Chin, D., Scott, D.M.

(2008) Bioorg Med Chem Lett 18: 5249-5251

• PubMed: 18778938 
• DOI: https://doi.org/10.1016/j.bmcl.2008.08.061
• Primary Citation Related Structures: 
  3BQM


• PubMed Abstract: 
  

  A series of meta-substituted anilines were designed and synthesized to inhibit the interaction of LFA-1 with ICAM for the treatment of autoimmune disease. Design of these molecules was performed by utilizing a co-crystal structure for structure-based drug design. The resulting molecules were found to be potent and to possess favorable pharmaceutical properties.

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Organizational Affiliation: 
• Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.59 kDa 
• Atom Count: 3,323 
• Modeled Residue Count: 364 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-L	A [auth B], B [auth C]	182	Homo sapiens	Mutation(s): 1  Gene Names: ITGAL, CD11A
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens) Explore P20701  Go to UniProtKB:  P20701
PHAROS:  P20701 GTEx:  ENSG00000005844

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BQM	C [auth B], D [auth C]	3-({4-[(1E)-3-morpholin-4-yl-3-oxoprop-1-en-1-yl]-2,3-bis(trifluoromethyl)phenyl}sulfanyl)aniline C21 H18 F6 N2 O2 S KLSZVPNVFKKIRD-FNORWQNLSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BQM	BindingDB:  3BQM	IC50: 1.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.284 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.535	α = 90
b = 70.505	β = 90
c = 72.558	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Silvian, L.F.

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations