4EHR | pdb_00004ehr

Crystal structure of Bcl-Xl complex with 4-(5-butyl-3-(hydroxymethyl)-1-phenyl-1h-pyrazol-4-yl)-3-(3,4-dihydro-2(1h)-isoquinolinylcarbonyl)-n-((2-(trimethylsilyl)ethyl)sulfonyl)benzamide

• PDB DOI: https://doi.org/10.2210/pdb4EHR/pdb

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


• Deposited: 2012-04-03 Released: 2012-06-06 
• Deposition Author(s): Schroeder, G.M., Wei, D., Banfi, P., Cai, Z., Lippy, J., Menichincheri, M., Modugno, M., Naglich, J., Penhallow, B., Perez, H.L., Sack, J., Schmidt, R.J., Tebben, A., Yan, C., Zhang, L., Galvani, A., Lombardo, L.J., Borzilleri, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

Pyrazole and pyrimidine phenylacylsulfonamides as dual Bcl-2/Bcl-xL antagonists.

Schroeder, G.M., Wei, D., Banfi, P., Cai, Z.W., Lippy, J., Menichincheri, M., Modugno, M., Naglich, J., Penhallow, B., Perez, H.L., Sack, J., Schmidt, R.J., Tebben, A., Yan, C., Zhang, L., Galvani, A., Lombardo, L.J., Borzilleri, R.M.

(2012) Bioorg Med Chem Lett 22: 3951-3956

• PubMed: 22608393 
• DOI: https://doi.org/10.1016/j.bmcl.2012.04.106
• Primary Citation Related Structures: 
  4EHR


• PubMed Abstract: 
  

  5-Butyl-1,4-diphenyl pyrazole and 2-amino-5-chloro pyrimidine acylsulfonamides were developed as potent dual antagonists of Bcl-2 and Bcl-xL. Compounds were optimized for binding to the I88, L92, I95, and F99 pockets normally occupied by pro-apoptotic protein Bim. An X-ray crystal structure confirmed the proposed binding mode. Observation of cytochrome c release from isolated mitochondria in MV-411 cells provides further evidence of target inhibition. Compounds demonstrated submicromolar antiproliferative activity in Bcl-2/Bcl-xL dependent cell lines.

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Organizational Affiliation: 
• Bristol-Myers Squibb Research, PO Box 4000, Princeton, NJ 08543-4000, USA. [e-mail]

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: 20.34 kDa 
• Atom Count: 1,171 
• Modeled Residue Count: 139 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A	172	Homo sapiens	Mutation(s): 0  Gene Names: BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0Q5	B [auth A]	4-[5-butyl-3-(hydroxymethyl)-1-phenyl-1H-pyrazol-4-yl]-3-(3,4-dihydroisoquinolin-2(1H)-ylcarbonyl)-N-{[2-(trimethylsilyl)ethyl]sulfonyl}benzamide C36 H44 N4 O5 S Si KDMMHDWLRNJPDK-UHFFFAOYSA-N
IMD	C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.227	α = 90
b = 102.227	β = 90
c = 34.929	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Schroeder, G.M., Wei, D., Banfi, P., Cai, Z., Lippy, J., Menichincheri, M., Modugno, M., Naglich, J., Penhallow, B., Perez, H.L., Sack, J., Schmidt, R.J., Tebben, A., Yan, C., Zhang, L., Galvani, A., Lombardo, L.J., Borzilleri, R.M.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-06-13
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations