6GMQ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.755 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.205 

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:  

  • 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.,Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongin-B
A, D, G, J
104Homo sapiensMutation(s): 0 
Gene Names: ELOB (TCEB2)
Find proteins for Q15370 (Homo sapiens)
Go to Gene View: ELOB
Go to UniProtKB:  Q15370
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Elongin-C
B, E
97Homo sapiensMutation(s): 0 
Gene Names: ELOC (TCEB1)
Find proteins for Q15369 (Homo sapiens)
Go to Gene View: ELOC
Go to UniProtKB:  Q15369
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
von Hippel-Lindau disease tumor suppressor
C, F, I, L
162Homo sapiensMutation(s): 0 
Gene Names: VHL
Find proteins for P40337 (Homo sapiens)
Go to Gene View: VHL
Go to UniProtKB:  P40337
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Elongin-C
H, K
97Homo sapiensMutation(s): 0 
Gene Names: ELOC (TCEB1)
Find proteins for Q15369 (Homo sapiens)
Go to Gene View: ELOC
Go to UniProtKB:  Q15369
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download SDF File 
Download CCD File 
F, I, L
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
F4K
Query on F4K
Download SDF File 
Download CCD File 
I, L
(4-pyrrol-1-ylphenyl)methanol
C11 H11 N O
LQQQPLUFBVYLRE-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA
Download SDF File 
Download CCD File 
I, L
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A, B, C, D, E, F, G, I, J, L
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.755 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.205 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.830α = 90.00
b = 93.830β = 90.00
c = 363.820γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-09-05
    Type: Data collection, Database references