6UVD

Crystal structure of BCL-XL bound to compound 2: (2R)-3-(Benzylsulfanyl)-2-({[(4-methylphenyl)methyl] [(4 phenylphenyl)carbonyl] carbamoyl}amino) propanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure-Guided Development of Potent Benzoylurea Inhibitors of BCL-X L and BCL-2.

Roy, M.J.Vom, A.Okamoto, T.Smith, B.J.Birkinshaw, R.W.Yang, H.Abdo, H.White, C.A.Segal, D.Huang, D.C.S.Baell, J.B.Colman, P.M.Czabotar, P.E.Lessene, G.

(2021) J Med Chem 64: 5447-5469

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01771
  • Primary Citation of Related Structures:  
    6UVC, 6UVD, 6UVE, 6UVF, 6UVG, 6UVH

  • PubMed Abstract: 

    The BCL-2 family of proteins (including the prosurvival proteins BCL-2, BCL-X L , and MCL-1) is an important target for the development of novel anticancer therapeutics. Despite the challenges of targeting protein-protein interaction (PPI) interfaces with small molecules, a number of inhibitors (called BH3 mimetics) have entered the clinic and the BCL-2 inhibitor, ABT-199/venetoclax, is already proving transformative. For BCL-X L , new validated chemical series are desirable. Here, we outline the crystallography-guided development of a structurally distinct series of BCL-X L /BCL-2 inhibitors based on a benzoylurea scaffold, originally proposed as α-helix mimetics. We describe structure-guided exploration of a cryptic "p5" pocket identified in BCL-X L . This work yields novel inhibitors with submicromolar binding, with marked selectivity toward BCL-X L . Extension into the hydrophobic p2 pocket yielded the most potent inhibitor in the series, binding strongly to BCL-X L and BCL-2 (nanomolar-range half-maximal inhibitory concentration (IC 50 )) and displaying mechanism-based killing in cells engineered to depend on BCL-X L for survival.


  • Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2-like protein 1
A, B
158Homo sapiensMutation(s): 0 
Gene Names: BCL2L1BCL2LBCLX
UniProt & NIH Common Fund Data Resources
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 GroupQ07817
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XOU (Subject of Investigation/LOI)
Query on XOU

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
(2R)-3-(Benzylsulfanyl)-2-({[(4-methylphenyl)methyl] [(4 phenylphenyl)carbonyl] carbamoyl}amino) propanoic acid
C32 H30 N2 O4 S
DCCZUUDOXXRWAG-LJAQVGFWSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.149α = 90
b = 97.149β = 90
c = 74.235γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-05-12
    Changes: Database references
  • Version 1.2: 2021-05-26
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description