8U27 | pdb_00008u27

Bcl-2-xL complexed with compound 35

  • Classification: APOPTOSIS
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2023-09-05 Released: 2023-09-13 
  • Deposition Author(s): Rizo, J., Pan, Y.-Z.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 4497 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 8U27

This is version 1.2 of the entry. See complete history

Literature

Structural insights for selective disruption of Beclin 1 binding to Bcl-2.

Pan, Y.Z.Liang, Q.Tomchick, D.R.De Brabander, J.K.Rizo, J.

(2023) Commun Biol 6: 1080-1080

  • DOI: https://doi.org/10.1038/s42003-023-05467-w
  • Primary Citation Related Structures: 
    8U27

  • PubMed Abstract: 

    Stimulation of autophagy could provide powerful therapies for multiple diseases, including cancer and neurodegeneration. An attractive drug target for this purpose is Bcl-2, which inhibits autophagy by binding to the Beclin 1 BH3-domain. However, compounds that preclude Beclin 1/Bcl-2 binding might also induce apoptosis, which is inhibited by binding of Bcl-2 to BH3-domains of pro-apoptosis factors such as Bax. Here we describe the NMR structure of Bcl-2 bound to 35, a compound that we recently found to inhibit Beclin 1/Bcl-2 binding more potently than Bax/Bcl-2 binding. The structure shows that 35 binds at one end of the BH3-binding groove of Bcl-2. Interestingly, much of the 35-binding site is not involved in binding to Bcl-2 inhibitors described previously and mediates binding to Beclin 1 but not Bax. The structure suggests potential avenues to design compounds that disrupt Beclin 1/Bcl-2 binding and stimulate autophagy without inducing apoptosis.


  • Organizational Affiliation
    • Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.

Macromolecule Content 

  • Total Structure Weight: 21.2 kDa 
  • Atom Count: 1,491 
  • Modeled Residue Count: 177 
  • Deposited Residue Count: 177 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-2, Bcl-2-like protein 1 chimera177Homo sapiensMutation(s): 0 
Gene Names: BCL2BCL2L1BCL2LBCLX
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ07817P10415
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ULL
(Subject of Investigation/LOI)

Query on ULL



Download:Ideal Coordinates CCD File
B [auth A]propan-2-yl {4-[(5S)-1-(4-bromobenzoyl)-5-phenyl-4,5-dihydro-1H-pyrazol-3-yl]phenyl}carbamate
C26 H24 Br N3 O3
RWCWONWFSWXBCW-DEOSSOPVSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 4497 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19AI142784

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Database references