2O7N

CD11A (LFA1) I-domain complexed with 7A-[(4-cyanophenyl)methyl]-6-(3,5-dichlorophenyl)-5-oxo-2,3,5,7A-tetrahydro-1H-pyrrolo[1,2-A]pyrrole-7-carbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Design of LFA-1 antagonists based on a 2,3-dihydro-1H-pyrrolizin-5(7aH)-one scaffold.

Dodd, D.S.Sheriff, S.Chang, C.J.Stetsko, D.K.Phillips, L.M.Zhang, Y.Launay, M.Potin, D.Vaccaro, W.Poss, M.A.McKinnon, M.Barrish, J.C.Suchard, S.J.Murali Dhar, T.G.

(2007) Bioorg Med Chem Lett 17: 1908-1911

  • DOI: https://doi.org/10.1016/j.bmcl.2007.01.036
  • Primary Citation of Related Structures:  
    2O7N

  • PubMed Abstract: 

    A new class of lymphocyte function-associated antigen-1 (LFA-1) antagonists is described. Elaboration of the 2,3-dihydro-1H-pyrrolizin-5(7aH)-one scaffold resulted in the synthesis of potent inhibitors of the LFA-1/ICAM-1 interaction. Along with the in vitro activity, we present the X-ray crystal structure of the complex of compound 9b, in a novel binding mode to the I-domain of LFA-1.


  • Organizational Affiliation

    Bristol-Myers Squibb Pharmaceutical Research Institute, P.O. Box 4000, Princeton, NJ 08543-4000, USA. dharmpal.dodd@bms.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-L183Homo sapiensMutation(s): 0 
Gene Names: ITGALCD11A
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2O7
Query on 2O7

Download Ideal Coordinates CCD File 
B [auth A]7A-[(4-cyanophenyl)methyl]-6-(3,5-dichlorophenyl)-5-oxo-2,3,5,7A-tetrahydro-1H-pyrrolo[1,2-A]pyrrole-7-carbonitrile
C22 H15 Cl2 N3 O
TZCXQSNBTXDAJG-QFIPXVFZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2O7 PDBBind:  2O7N IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.6α = 90
b = 88.4β = 90
c = 71.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
AMoREphasing
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2007-03-20 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description