4C52

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.049 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

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

  • DOI: 10.1021/jm401948b
  • Primary Citation of Related Structures:  

  • 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 ...

    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.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BCL-2-LIKE PROTEIN 1
A, B
158Homo sapiensMutation(s): 0 
Gene Names: BCL2L1 (BCL2L, BCLX)
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
X0D
Query on X0D
Download SDF File 
Download CCD File 
A, 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
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
X0DIC50: 22000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.049 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.159 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.814α = 90.00
b = 63.814β = 90.00
c = 132.830γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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