2ICA

CD11a (LFA1) I-domain complexed with BMS-587101 aka 5-[(5S, 9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro [4.4]non-7-yl]methyl]-3-thiophenecarboxylicacid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2ICClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Discovery and Development of 5-[(5S,9R)-9- (4-Cyanophenyl)-3-(3,5-dichlorophenyl)-1- methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]non- 7-yl-methyl]-3-thiophenecarboxylic acid (BMS-587101)-A Small Molecule Antagonist Leukocyte Function Associated Antigen-1.

Potin, D.Launay, M.Monatlik, F.Malabre, P.Fabreguettes, M.Fouquet, A.Maillet, M.Nicolai, E.Dorgeret, L.Chevallier, F.Besse, D.Dufort, M.Caussade, F.Ahmad, S.Z.Stetsko, D.K.Skala, S.Davis, P.M.Balimane, P.Patel, K.Yang, Z.Marathe, P.Postelneck, J.Townsend, R.M.Goldfarb, V.Sheriff, S.Einspahr, H.Kish, K.Malley, M.F.Dimarco, J.D.Gougoutas, J.Z.Kadiyala, P.Cheney, D.L.Tejwani, R.W.Murphy, D.K.McIntyre, K.W.Yang, X.Chao, S.Leith, L.Xiao, Z.Mathur, A.Chen, B.C.Wu, D.R.Traeger, S.C.McKinnon, M.Barrish, J.C.Robl, J.A.Iwanowicz, E.J.Suchard, S.J.Dhar, T.G.

(2006) J Med Chem 49: 6946-6949

  • DOI: https://doi.org/10.1021/jm0610806
  • Primary Citation of Related Structures:  
    2ICA

  • PubMed Abstract: 

    LFA-1 (leukocyte function-associated antigen-1), is a member of the beta2-integrin family and is expressed on all leukocytes. This letter describes the discovery and preliminary SAR of spirocyclic hydantoin based LFA-1 antagonists that culminated in the identification of analog 8 as a clinical candidate. We also report the first example of the efficacy of a small molecule LFA-1 antagonist in combination with CTLA-4Ig in an animal model of transplant rejection.


  • Organizational Affiliation

    Cerep, 19 avenue du Quebec, 91951 Courtaboeuf cedex, France.


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
2IC
Query on 2IC

Download Ideal Coordinates CCD File 
B [auth A]5-[(5S,9R)-9-(4-CYANOPHENYL)-3-(3,5-DICHLOROPHENYL)-1-METHYL-2,4-DIOXO-1,3,7-TRIAZASPIRO [4.4]NON-7-YL]METHYL]-3-THIOPHENECARBOXYLICACID
C26 H20 Cl2 N4 O4 S
NXNKJLOEGWSJGI-BKMJKUGQSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2IC BindingDB:  2ICA IC50: min: 18, max: 280 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.3α = 90
b = 63.4β = 90
c = 63.3γ = 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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 2ICClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-19
    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: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description