3M6F | pdb_00003m6f

CD11A I-domain complexed with 6-((5S,9R)-9-(4-CYANOPHENYL)-3-(3,5-DICHLOROPHENYL)-1-METHYL-2,4-DIOXO-1,3,7- TRIAZASPIRO[4.4]NON-7-YL)NICOTINIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.227 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3M6F

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Small molecule antagonist of leukocyte function associated antigen-1 (LFA-1): structure-activity relationships leading to the identification of 6-((5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]nonan-7-yl)nicotinic acid (BMS-688521).

Watterson, S.H.Xiao, Z.Dodd, D.S.Tortolani, D.R.Vaccaro, W.Potin, D.Launay, M.Stetsko, D.K.Skala, S.Davis, P.M.Lee, D.Yang, X.McIntyre, K.W.Balimane, P.Patel, K.Yang, Z.Marathe, P.Kadiyala, P.Tebben, A.J.Sheriff, S.Chang, C.Y.Ziemba, T.Zhang, H.Chen, B.C.DelMonte, A.J.Aranibar, N.McKinnon, M.Barrish, J.C.Suchard, S.J.Murali Dhar, T.G.

(2010) J Med Chem 53: 3814-3830

  • DOI: https://doi.org/10.1021/jm100348u
  • Primary Citation Related Structures: 
    3M6F

  • PubMed Abstract: 

    Leukocyte function-associated antigen-1 (LFA-1), also known as CD11a/CD18 or alpha(L)beta(2), belongs to the beta(2) integrin subfamily and is constitutively expressed on all leukocytes. The major ligands of LFA-1 include three intercellular adhesion molecules 1, 2, and 3 (ICAM 1, 2, and 3). The interactions between LFA-1 and the ICAMs are critical for cell adhesion, and preclinical animal studies and clinical data from the humanized anti-LFA-1 antibody efalizumab have provided proof-of-concept for LFA-1 as an immunological target. This article will detail the structure-activity relationships (SAR) leading to a novel second generation series of highly potent spirocyclic hydantoin antagonists of LFA-1. With significantly enhanced in vitro and ex vivo potency relative to our first clinical compound (1), as well as demonstrated in vivo activity and an acceptable pharmacokinetic and safety profile, 6-((5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro-[4.4]nonan-7-yl)nicotinic acid (2e) was selected to advance into clinical trials.


  • Organizational Affiliation
    • Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, USA. scott.watterson@bms.com

Macromolecule Content 

  • Total Structure Weight: 21.53 kDa 
  • Atom Count: 1,595 
  • Modeled Residue Count: 180 
  • 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: 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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BJZ

Query on BJZ



Download:Ideal Coordinates CCD File
B [auth A]6-[(5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]non-7-yl]pyridine-3-carboxylic acid
C26 H19 Cl2 N5 O4
LILGMDXLRPEBNH-HFZDXXHNSA-N
NO3

Query on NO3



Download:Ideal Coordinates CCD File
C [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.227 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.6α = 90
b = 63.6β = 90
c = 63.1γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2010-05-12 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-04-04
    Changes: Advisory, Data collection
  • Version 1.3: 2018-04-11
    Changes: Data collection
  • Version 1.4: 2023-09-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description