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 

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Ligand Structure Quality Assessment 


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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: 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 ...

    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 Degradation Group, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence 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)
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Go to UniProtKB:  P40337
PHAROS:  P40337
Entity Groups  
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UniProt GroupP40337
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-BB [auth BBB]107Homo sapiensMutation(s): 0 
Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
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PHAROS:  Q15370
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UniProt GroupQ15370
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-CC [auth CCC]96Homo sapiensMutation(s): 0 
Gene Names: ELOC, TCEB1
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Find proteins for Q15369 (Homo sapiens)
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PHAROS:  Q15369
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UniProt GroupQ15369
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2-like protein 1D [auth DDD]221Homo sapiensMutation(s): 0 
Gene Names: BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
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UniProt GroupQ07817
Protein Feature View
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Small Molecules
Ligands 4 Unique
IDChainsName / 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		 Ligand Interaction
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		 Ligand Interaction
GOL
Query on GOL
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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		 Ligand Interaction
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		 Ligand Interaction
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

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Ligand Structure Quality Assessment 


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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