8BDX

Ternary complex between VCB, BRD4-BD2 and PROTAC 48


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Systematic Potency and Property Assessment of VHL Ligands and Implications on PROTAC Design.

Krieger, J.Sorrell, F.J.Wegener, A.A.Leuthner, B.Machrouhi-Porcher, F.Hecht, M.Leibrock, E.M.Muller, J.E.Eisert, J.Hartung, I.V.Schlesiger, S.

(2023) ChemMedChem 18: e202200615-e202200615

  • DOI: https://doi.org/10.1002/cmdc.202200615
  • Primary Citation of Related Structures:  
    8BDI, 8BDJ, 8BDL, 8BDM, 8BDN, 8BDO, 8BDS, 8BDT, 8BDX, 8BEB

  • PubMed Abstract: 

    Herein, we describe a systematic SAR- and SPR-investigation of the peptidomimetic hydroxy-proline based VHL-ligand VH032, from which most to-date published VHL-targeting PROTACs have been derived. This study provides for the first time a consistent data set which allows for direct comparison of structural variations including those which were so far hidden in patent literature. The gained knowledge about improved VHL binders was used to design a small library of highly potent BRD4-degraders comprising different VHL exit vectors. Newly designed degraders showed favorable molecular properties and significantly improved degradation potency compared to MZ1.


  • Organizational Affiliation

    Discovery and Development Technologies, Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4
A, E
129Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
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Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B
B, F
104Homo 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 
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UniProt GroupQ15370
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-C
C, G
97Homo 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 
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UniProt GroupQ15369
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressor
D, H
162Homo 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 
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UniProt GroupP40337
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QIY (Subject of Investigation/LOI)
Query on QIY

Download Ideal Coordinates CCD File 
I [auth D],
J [auth H]
(2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8$l^{5},11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2R)-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide
C50 H63 Cl2 N9 O9 S
FWYJZESSPDZGOM-YLIPSVQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.341α = 90
b = 82.341β = 90
c = 168.96γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2023-04-26
    Changes: Database references
  • Version 2.0: 2024-01-24
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-02-07
    Changes: Refinement description