4IEH

Crystal Structure of human Bcl-2 in complex with a small molecule inhibitor targeting Bcl-2 BH3 domain interactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The role of the acidity of N-heteroaryl sulfonamides as inhibitors of bcl-2 family protein-protein interactions.

Toure, B.B.Miller-Moslin, K.Yusuff, N.Perez, L.Dore, M.Joud, C.Michael, W.DiPietro, L.van der Plas, S.McEwan, M.Lenoir, F.Hoe, M.Karki, R.Springer, C.Sullivan, J.Levine, K.Fiorilla, C.Xie, X.Kulathila, R.Herlihy, K.Porter, D.Visser, M.

(2013) ACS Med Chem Lett 4: 186-190

  • DOI: 10.1021/ml300321d
  • Primary Citation of Related Structures:  
    4IEH

  • PubMed Abstract: 
  • Overexpression of the antiapoptotic members of the Bcl-2 family of proteins is commonly associated with cancer cell survival and resistance to chemotherapeutics. Here, we describe the structure-based optimization of a series of N-heteroaryl sulfonamides that demonstrate potent mechanism-based cell death ...

    Overexpression of the antiapoptotic members of the Bcl-2 family of proteins is commonly associated with cancer cell survival and resistance to chemotherapeutics. Here, we describe the structure-based optimization of a series of N-heteroaryl sulfonamides that demonstrate potent mechanism-based cell death. The role of the acidic nature of the sulfonamide moiety as it relates to potency, solubility, and clearance is examined. This has led to the discovery of novel heterocyclic replacements for the acylsulfonamide core of ABT-737 and ABT-263.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research Inc. , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-2, Bcl-2-like protein 1 chimeraA169Homo sapiensMutation(s): 0 
Gene Names: BCL2BCL2LBCL2L1BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
Find proteins for P10415 (Homo sapiens)
Explore P10415 
Go to UniProtKB:  P10415
PHAROS:  P10415
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1E9 (Subject of Investigation/LOI)
Query on 1E9

Download Ideal Coordinates CCD File 
B [auth A]N-(6-{4-[(4'-chlorobiphenyl-2-yl)methyl]piperazin-1-yl}-1,1-dioxido-1,2-benzothiazol-3-yl)-4-{[(2R)-4-(dimethylamino)-1-(phenylsulfanyl)butan-2-yl]amino}-3-nitrobenzenesulfonamide
C42 H44 Cl N7 O6 S3
IXACTXFUQMBZJI-MGBGTMOVSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1E9 Binding MOAD:  4IEH Kd: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.529α = 90
b = 73.529β = 90
c = 96.205γ = 90
Software Package:
Software NamePurpose
PHASESphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2012-12-13 
  • Released Date: 2013-07-10 
  • Deposition Author(s): Xie, X., Kulathila, R.

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy