4IEH

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

• PDB DOI: https://doi.org/10.2210/pdb4IEH/pdb

• Classification: APOPTOSIS/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

---

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 

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

• PubMed: 24900652 
• DOI: https://doi.org/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. 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.51 kDa 
• Atom Count: 1,406 
• Modelled Residue Count: 138 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-2, Bcl-2-like protein 1 chimera	A	169	Homo sapiens	Mutation(s): 0  Gene Names: BCL2, BCL2L, BCL2L1, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552
Find proteins for P10415 (Homo sapiens) Explore P10415  Go to UniProtKB:  P10415
PHAROS:  P10415 GTEx:  ENSG00000171791
UniProt Groups	Q07817P10415

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1E9	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

Binding Affinity Annotations
ID	Source	Binding 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 = 73.529	α = 90
b = 73.529	β = 90
c = 96.205	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations