1XUO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA. sompong.wattanasin@pharma.novartis.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-L
A, B
188Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens)
Explore P20701 
Go to UniProtKB:  P20701
PHAROS:  P20701
GTEx:  ENSG00000005844 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20701
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LA1
Query on LA1

Download Ideal Coordinates CCD File 
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
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
LA1 BindingDB:  1XUO IC50: 69 (nM) from 1 assay(s)
PDBBind:  1XUO IC50: 69 (nM) from 1 assay(s)
Binding MOAD:  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 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.259α = 90
b = 59.995β = 90
c = 142.616γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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