9GIO | pdb_00009gio

Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of VHL.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.233 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of a Series of Covalent Ligands That Bind to Cys77 of the Von Hippel-Lindau Tumor Suppressor Protein (VHL).

Lucas, S.C.C.Xu, Y.Hewitt, S.Collie, G.W.Fusani, L.Kadamur, G.Hadfield, T.E.Su, N.Truman, C.Demanze, S.Hao, H.Phillips, C.

(2025) ACS Med Chem Lett 16: 693-699

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00582
  • Primary Citation Related Structures: 
    9GIO

  • PubMed Abstract: 

    Most ligands for the Von Hippel-Lindau tumor suppressor (VHL) bind at the HIF-1α binding site. Ligands that bind to allosteric sites on VHL could be highly valuable for the field of protein degradation, therefore, a covalent hit identification campaign was run targeting Cys77 on VHL. Hit 2 bound selectively to Cys77 on VHL and did not alkylate the reactive Cys89 on Elongin B. It showed time- and concentration-dependent labeling, with a k inact / K I of 0.30 M -1 s -1 , and does not affect binding at the HIF-1α site. This hit ligand was optimized to afford compound 15 which showed improved potency and labeling of VHL. An X-ray structure of a close analogue was determined revealing the compound binding in a shallow groove on the surface of VHL. These are the first small molecules that bind covalently to an allosteric site on VHL and provide a suitable starting point for further optimization.


  • Organizational Affiliation
    • Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB2 0AA, U.K.

Macromolecule Content 

  • Total Structure Weight: 42.27 kDa 
  • Atom Count: 3,043 
  • Modeled Residue Count: 334 
  • Deposited Residue Count: 363 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-B107Homo 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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Elongin-C96Homo 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
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressor160Homo 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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3JF

Query on 3JF



Download:Ideal Coordinates CCD File
D [auth C]N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide
C24 H32 N4 O4 S
GFVIEZBZIUKYOG-SVFBPWRDSA-N
A1IMD

Query on A1IMD



Download:Ideal Coordinates CCD File
E [auth C]N-[2-(dimethylsulfamoyl)-5-[(1-methylpyrazol-4-yl)methoxy]phenyl]propanamide
C16 H22 N4 O4 S
LQSCXKPWVDQSNE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.233 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.781α = 90
b = 59.312β = 100.12
c = 97.316γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-03-26 
  • Deposition Author(s): Collie, G.W.

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references