1XUO

X-ray structure of LFA-1 I-domain bound to a 1,4-diazepane-2,5-dione inhibitor at 1.8A resolution

• PDB DOI: https://doi.org/10.2210/pdb1XUO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-10-26 Released: 2005-10-26 
• Deposition Author(s): Wattanasin, S., Kallen, J., Myers, S., Guo, Q., Sabio, M., Ehrhardt, C., Albert, R., Hommel, U., Weckbecker, G., Welzenbach, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

1,4-Diazepane-2,5-diones as novel inhibitors of LFA-1

Wattanasin, S., Kallen, J., Myers, S., Guo, Q., Sabio, M., Ehrhardt, C., Albert, R., Hommel, U., Weckbecker, G., Welzenbach, K., Weitz-Schmidt, G.

(2005) Bioorg Med Chem Lett 15: 1217-1220

• PubMed: 15686945 
• DOI: https://doi.org/10.1016/j.bmcl.2004.11.072
• Primary Citation of Related Structures:  
  1XUO


• PubMed Abstract: 
  

  1,4-Diazepane-2,5-diones (2) are found to be a new class of potent LFA-1 inhibitors. The synthesis, structure, and biological evaluation of these 1,4-diazepine-2,5-diones and related derivatives are described.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, Cambridge, MA 02139, 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.

Macromolecule Content

• Total Structure Weight: 43.44 kDa 
• Atom Count: 3,154 
• Modelled Residue Count: 356 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-L	A, B	188	Homo sapiens	Mutation(s): 0
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LA1	D [auth A]	(2R)-2-[3-ISOBUTYL-2,5-DIOXO-4-(QUINOLIN-3-YLMETHYL)-1,4-DIAZEPAN-1-YL]-N-METHYL-3-(2-NAPHTHYL)PROPANAMIDE C33 H36 N4 O3 COVPLULNDBDXTN-KYJUHHDHSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LA1	BindingDB:  1XUO	IC50: 69 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.259	α = 90
b = 59.995	β = 90
c = 142.616	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-26 
Deposition Author(s): Wattanasin, S., Kallen, J., Myers, S., Guo, Q., Sabio, M., Ehrhardt, C., Albert, R., Hommel, U., Weckbecker, G., Welzenbach, K.

Revision History  

• Version 1.0: 2005-10-26
  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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-03-20
  Changes: Source and taxonomy, Structure summary