4AQ3 | pdb_00004aq3

HUMAN BCL-2 WITH PHENYLACYLSULFONAMIDE INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb4AQ3/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-04-12 Released: 2012-06-06 
• Deposition Author(s): Bertrand, J.A., Fasolini, M., Modugno, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: other

Literature

Identification of a Phenylacylsulfonamide Series of Dual Bcl-2/Bcl-Xl Antagonists.

Perez, H.L., Banfi, P., Bertrand, J.A., Cai, Z.W., Grebinski, J.W., Kim, K., Lippy, J., Modugno, M., Naglich, J., Schmidt, R.J., Tebben, A., Vianello, P., Wei, D.D., Zhang, L., Galvani, A., Lombardo, L.J., Borzilleri, R.M.

(2012) Bioorg Med Chem Lett 22: 3946

• PubMed: 22608961 
• DOI: https://doi.org/10.1016/j.bmcl.2012.04.103
• Primary Citation Related Structures: 
  4AQ3


• PubMed Abstract: 
  

  A series of phenylacylsulfonamides has been prepared as antagonists of Bcl-2/Bcl-xL. In addition to potent binding affinities for both Bcl-2 and Bcl-xL, these compounds were shown to induce classical markers of apoptosis in isolated mitochondria. Overall weak cellular potency was improved by the incorporation of polar functionality resulting in compounds with moderate antiproliferative activity.

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

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 122.26 kDa 
• Atom Count: 7,096 
• Modeled Residue Count: 814 
• Deposited Residue Count: 1,014 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1	A, B, C, D, E, F	169	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P10415 (Homo sapiens) Explore P10415  Go to UniProtKB:  P10415
PHAROS:  P10415 GTEx:  ENSG00000171791
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552
UniProt Groups	Q07817P10415

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
398	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	N,N-dibutyl-4-chloranyl-1-[2-(3,4-dihydro-1H-isoquinolin-2-ylcarbonyl)-4-[(7-iodanylnaphthalen-2-yl)sulfonylcarbamoyl]phenyl]-5-methyl-pyrazole-3-carboxamide C40 H41 Cl I N5 O5 S DKJBPPVETUSFTM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.214	α = 90
b = 115.214	β = 90
c = 102.318	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Bertrand, J.A., Fasolini, M., Modugno, M.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description