6ZHC

PROTAC6 mediated complex of VHL:EloB:EloC and Bcl-xL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Insights into PROTAC-Mediated Degradation of Bcl-xL.

Chung, C.W.Dai, H.Fernandez, E.Tinworth, C.P.Churcher, I.Cryan, J.Denyer, J.Harling, J.D.Konopacka, A.Queisser, M.A.Tame, C.J.Watt, G.Jiang, F.Qian, D.Benowitz, A.B.

(2020) ACS Chem Biol 15: 2316-2323

  • DOI: https://doi.org/10.1021/acschembio.0c00266
  • Primary Citation of Related Structures:  
    6ZHC

  • PubMed Abstract: 

    The Bcl-2 family of proteins, such as Bcl-xL and Bcl-2, play key roles in cancer cell survival. Structural studies of Bcl-xL formed the foundation for the development of the first Bcl-2 family inhibitors and FDA approved drugs. Recently, Pro teolysis Ta rgeting C himeras (PROTACs) that degrade Bcl-xL have been proposed as a therapeutic modality with the potential to enhance potency and reduce toxicity versus antagonists. However, no ternary complex structures of Bcl-xL with a PROTAC and an E3 ligase have been successfully determined to guide this approach. Herein, we report the design, characterization, and X-ray structure of a VHL E3 ligase-recruiting Bcl-xL PROTAC degrader. The 1.9 Å heterotetrameric structure, composed of (ElonginB:ElonginC:VHL):PROTAC:Bcl-xL, reveals an extensive network of neo-interactions, between the E3 ligase and the target protein, and between noncognate parts of the PROTAC and partner proteins. This work illustrates the challenges associated with the rational design of bifunctional molecules where interactions involve composite interfaces.


  • Organizational Affiliation

    Protein, Cellular & Structural Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressorA [auth AAA]155Homo sapiensMutation(s): 0 
Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens)
Explore P40337 
Go to UniProtKB:  P40337
PHAROS:  P40337
GTEx:  ENSG00000134086 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40337
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-BB [auth BBB]107Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
PHAROS:  Q15370
GTEx:  ENSG00000103363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15370
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CC [auth CCC]96Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15369
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2-like protein 1D [auth DDD]221Homo 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  
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UniProt GroupQ07817
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QL8 (Subject of Investigation/LOI)
Query on QL8

Download Ideal Coordinates CCD File 
E [auth AAA]2-[8-(1,3-benzothiazol-2-ylcarbamoyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]-5-[3-[4-[3-[2-[2-[2-[2-[2-[3-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]prop-1-ynyl]phenoxy]propyl]-1,3-thiazole-4-carboxylic acid
C68 H80 N8 O14 S3
LOJJAKUNUJJOKC-MXEISZGISA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
FA [auth CCC]
GA [auth CCC]
HA [auth CCC]
O [auth AAA]
P [auth AAA]
FA [auth CCC],
GA [auth CCC],
HA [auth CCC],
O [auth AAA],
P [auth AAA],
PA [auth DDD],
Q [auth AAA],
QA [auth DDD],
R [auth AAA],
S [auth AAA],
Y [auth BBB],
Z [auth BBB]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth CCC]
J [auth AAA]
K [auth AAA]
L [auth AAA]
M [auth AAA]
EA [auth CCC],
J [auth AAA],
K [auth AAA],
L [auth AAA],
M [auth AAA],
MA [auth DDD],
N [auth AAA],
NA [auth DDD],
OA [auth DDD]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth CCC]
BA [auth CCC]
CA [auth CCC]
DA [auth CCC]
F [auth AAA]
AA [auth CCC],
BA [auth CCC],
CA [auth CCC],
DA [auth CCC],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
IA [auth DDD],
JA [auth DDD],
KA [auth DDD],
LA [auth DDD],
T [auth BBB],
U [auth BBB],
V [auth BBB],
W [auth BBB],
X [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.99α = 90
b = 101.18β = 90
c = 106.93γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-08-05 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description