Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 38.26 kDa 
• Atom Count: 2637 
• Modelled Residue Count: 290 
• Deposited Residue Count: 316 
• Unique protein chains: 1

4C52

Crystal structure of Bcl-xL in complex with benzoylurea compound (39b)

• DOI: 10.2210/pdb4C52/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-10 Released: 2014-02-05 
• Deposition Author(s): Roy, M.J., Brady, R.M., Lessene, G., Colman, P.M., Czabotar, P.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.216 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 

Literature

De-Novo Designed Library of Benzoylureas as Inhibitors of Bcl-Xl: Synthesis, Structural and Biochemical Characterization.

Brady, R.M., Vom, A., Roy, M.J., Toovey, N., Smith, B.J., Moss, R.M., Hazis, E., Huang, D.C.S., Parisot, J.P., Yang, H., Street, I.P., Colman, P.M., Czabotar, P.E., Baell, J.B., Lessene, G.

(2014) J Med Chem 57: 1323

• PubMed: 24456288 
• DOI: 10.1021/jm401948b
• Primary Citation of Related Structures:  
  4C5D, 4C52


• PubMed Abstract: 
  

The prosurvival BCL-2 proteins are attractive yet challenging targets for medicinal chemists. Their involvement in the initiation and progression of many, if not all, tumors makes them prime targets for developing new anticancer therapies. We present our approach based on de novo structure-based drug design. Using known structural information from complexes engaging opposing members of the BCL-2 family of proteins, we designed peptidomimetic compounds using a benzoylurea scaffold to reproduce key interactions between these proteins. A library stemming from the initial de novo designed scaffold led to the discovery of ligands with low micromolar potency (KD = 4 μM) and selectivity for BCL-XL. These compounds bind in the canonical BH3 binding groove in a binding mode distinct from previously known BCL-2 inhibitors. The results of our study provide insight into the design of a new class of antagonists targeting a challenging class of protein-protein interactions.

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Organizational Affiliation: 

The Walter and Eliza Hall Institute of Medical Research , 1G Royal Parade, Parkville, Victoria 3052, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL-2-LIKE PROTEIN 1	A, B	158	Homo sapiens	Mutation(s): 0  Gene Names: BCL2L1, BCL2L, BCLX
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
NIH Common Fund Data Resources
PHAROS:  Q07817 GTEx:  ENSG00000171552

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X0D	C [auth A], N [auth B]	(R)-2-(3-(3-((2,4-DIFLUOROPENYL)ETHYNYL)BENZOYL)-3-PROPYLUREIDO)-3-(ISOBUTYLTHIO) PROPANOIC ACID C26 H28 F2 N2 O4 S KBNODIQMRDIBMX-QHCPKHFHSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], O [auth B], P [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
X0D	Kd:  2100   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.216 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.814	α = 90
b = 63.814	β = 90
c = 132.83	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-10 
• Released Date: 2014-02-05 
Deposition Author(s): Roy, M.J., Brady, R.M., Lessene, G., Colman, P.M., Czabotar, P.E.

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2014-03-12
  Changes: Database references
• Version 1.2: 2015-04-29
  Changes: Data collection