6GMR

pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase.

Lucas, X.Van Molle, I.Ciulli, A.

(2018) J Med Chem 61: 7387-7393

  • DOI: 10.1021/acs.jmedchem.8b00842
  • Primary Citation of Related Structures:  
    6GMX, 6GMN, 6GMQ, 6GMR

  • PubMed Abstract: 
  • Beyond the targeting of E3 ubiquitin ligases to inhibit protein homeostasis, E3 ligase binders can be repurposed as targeted protein degraders (PROTACs or molecular glues). We sought to identify new binders of the VHL E3 ligase by biophysical fragmen ...

    Beyond the targeting of E3 ubiquitin ligases to inhibit protein homeostasis, E3 ligase binders can be repurposed as targeted protein degraders (PROTACs or molecular glues). We sought to identify new binders of the VHL E3 ligase by biophysical fragment-based screening followed by X-ray crystallographic soaking. We identified fragments binding at the ElonginC:Cullin2 interface and a new cryptic pocket in VHL, along with other potential ligandable sites predicted computationally and found to bind solvent molecules in crystal structures. The elucidated interactions provide starting points for future ligand development.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, James Black Centre, School of Life Sciences , University of Dundee , Dow Street , Dundee , DD1 5EH , United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-BB118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
NIH Common Fund Data Resources
PHAROS  Q15370
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-CC97Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
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PHAROS  Q15369
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Hypoxia inducible factor 1alpha, residues 559-577H19Homo sapiensMutation(s): 0 
Gene Names: HIF1ABHLHE78MOP1PASD8
Find proteins for Q16665 (Homo sapiens)
Explore Q16665 
Go to UniProtKB:  Q16665
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PHAROS  Q16665
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressorV163Homo sapiensMutation(s): 0 
Gene Names: VHL
Find proteins for P40337 (Homo sapiens)
Explore P40337 
Go to UniProtKB:  P40337
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PHAROS  P40337
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F4K
Query on F4K

Download CCD File 
V
(4-pyrrol-1-ylphenyl)methanol
C11 H11 N O
LQQQPLUFBVYLRE-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
V
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
HL-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.88α = 90
b = 59.88β = 90
c = 246.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
BUSTER-TNTphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilERC-2012-StG-311460
European CommissionH2020-MSCA-IF-2015-806323
European CommissionEC PIEF-GA-2010-275683
United Kingdomwelcome trust 100476/Z/12/Z
United Kingdomwelcome trust 094090/Z/10/Z

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references