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⇱ RCSB PDB - 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

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Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 2ICA | pdb_00002ica

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), 0.229 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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wwPDB Validation3D Report Full Report


Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 21.49 kDa 
  • Atom Count: 1,595 
  • Modeled Residue Count: 179 
  • Deposited Residue Count: 183 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin alpha-L183Homo sapiensMutation(s): 0 
Gene Names: ITGAL, CD11A
👁 Image
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
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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		👁 Image

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.223 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.197 (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

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Ligand Structure Quality Assessment 


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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.