2W3L

Crystal Structure of Chimaeric Bcl2-xL and Phenyl Tetrahydroisoquinoline Amide Complex

• PDB DOI: https://doi.org/10.2210/pdb2W3L/pdb

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


• Deposited: 2008-11-13 Released: 2008-12-09 
• Deposition Author(s): Porter, J., Payne, A., de Candole, B., Ford, D., Hutchinson, B., Trevitt, G., Turner, J., Edwards, C., Watkins, C., Whitcombe, I., Davis, J., Stubberfield, C., Fisher, M., Lamers, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.258 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Tetrahydroisoquinoline Amide Substituted Phenyl Pyrazoles as Selective Bcl-2 Inhibitors.

Porter, J., Payne, A., De Candole, B., Ford, D., Hutchinson, B., Trevitt, G., Turner, J., Edwards, C., Watkins, C., Whitcombe, I., Davis, J., Stubberfield, C.

(2009) Bioorg Med Chem Lett 19: 230

• PubMed: 19027294 
• DOI: https://doi.org/10.1016/j.bmcl.2008.10.113
• Primary Citation of Related Structures:  
  2W3L


• PubMed Abstract: 
  

  Anti-apoptotic Bcl-2 protects cells from apoptosis by binding to pro-apoptotic members of the Bcl-2 family thereby playing a role in tumour survival in response to chemo- or radiation therapy. We describe a series of phenyl pyrazoles that have high affinity for Bcl-2 and rationalise the observed SAR by means of an X-ray crystal structure.

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Organizational Affiliation: 

UCB Celltech, 216 Bath Road, Slough, United Kingdom. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.9 kDa 
• Atom Count: 2,625 
• Modelled Residue Count: 283 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APOPTOSIS REGULATOR BCL-2	A, B	144	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10415 (Homo sapiens) Explore P10415  Go to UniProtKB:  P10415
PHAROS:  P10415 GTEx:  ENSG00000171791

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DRO	C [auth A], D [auth B]	1-(2-{[(3S)-3-(aminomethyl)-3,4-dihydroisoquinolin-2(1H)-yl]carbonyl}phenyl)-4-chloro-5-methyl-N,N-diphenyl-1H-pyrazole-3-carboxamide C34 H30 Cl N5 O2 MLZCQGFPFQDFLC-NDEPHWFRSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DRO	PDBBind:  2W3L	IC50: 30 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.258 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68	α = 90
b = 68.32	β = 90
c = 70.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Porter, J., Payne, A., de Candole, B., Ford, D., Hutchinson, B., Trevitt, G., Turner, J., Edwards, C., Watkins, C., Whitcombe, I., Davis, J., Stubberfield, C., Fisher, M., Lamers, M.

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Other