3SP7

Crystal Structure of Bcl-xL bound to BM903

• PDB DOI: https://doi.org/10.2210/pdb3SP7/pdb

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


• Deposited: 2011-07-01 Released: 2012-07-04 
• Deposition Author(s): Meagher, J.L., Stuckey, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Structure-based design of a new class of potent Bcl-2/Bcl-xL inhibitors

Zhou, H., Chen, J., Meagher, J.L., Aguilar, A., Bai, L., Liu, L., Yang, C.Y., Xin, C., Stuckey, J.A., Wang, S.

To be published.

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: 21.02 kDa 
• Atom Count: 1,525 
• Modelled Residue Count: 150 
• 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: Bcl-xL, BCL2L, BCL2L1, 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
03B	B [auth A]	5-(4-chlorophenyl)-4-{3-[4-(4-{[(4-{[(2R)-4-(dimethylamino)-1-(phenylsulfanyl)butan-2-yl]amino}-3-nitrophenyl)sulfonyl]amino}phenyl)piperazin-1-yl]phenyl}-1,2-dimethyl-1H-pyrrole-3-carboxylic acid C47 H50 Cl N7 O6 S2 IUXZRSUDCUOHPK-DIPNUNPCSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	G [auth A], H [auth A], I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.627	α = 90
b = 54.891	β = 90
c = 79.569	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
MD2	data collection
HKL-2000	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-04 
Deposition Author(s): Meagher, J.L., Stuckey, J.A.

Revision History  

• Version 1.0: 2012-07-04
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations