5LLI

pVHL:EloB:EloC in complex with VH298


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Potent and selective chemical probe of hypoxic signalling downstream of HIF-alpha hydroxylation via VHL inhibition.

Frost, J.Galdeano, C.Soares, P.Gadd, M.S.Grzes, K.M.Ellis, L.Epemolu, O.Shimamura, S.Bantscheff, M.Grandi, P.Read, K.D.Cantrell, D.A.Rocha, S.Ciulli, A.

(2016) Nat Commun 7: 13312-13312

  • DOI: 10.1038/ncomms13312

  • PubMed Abstract: 
  • Chemical strategies to using small molecules to stimulate hypoxia inducible factors (HIFs) activity and trigger a hypoxic response under normoxic conditions, such as iron chelators and inhibitors of prolyl hydroxylase domain (PHD) enzymes, have broad ...

    Chemical strategies to using small molecules to stimulate hypoxia inducible factors (HIFs) activity and trigger a hypoxic response under normoxic conditions, such as iron chelators and inhibitors of prolyl hydroxylase domain (PHD) enzymes, have broad-spectrum activities and off-target effects. Here we disclose VH298, a potent VHL inhibitor that stabilizes HIF-α and elicits a hypoxic response via a different mechanism, that is the blockade of the VHL:HIF-α protein-protein interaction downstream of HIF-α hydroxylation by PHD enzymes. We show that VH298 engages with high affinity and specificity with VHL as its only major cellular target, leading to selective on-target accumulation of hydroxylated HIF-α in a concentration- and time-dependent fashion in different cell lines, with subsequent upregulation of HIF-target genes at both mRNA and protein levels. VH298 represents a high-quality chemical probe of the HIF signalling cascade and an attractive starting point to the development of potential new therapeutics targeting hypoxia signalling.


    Organizational Affiliation

    Center for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.,Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.,Cellzome GmbH, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor B polypeptide 2
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
Transcription elongation factor B polypeptide 1
B, E, 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
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6Z3
Query on 6Z3

Download SDF File 
Download CCD File 
C, F, I, L
(2~{S},4~{R})-1-[(2~{S})-2-[(1-cyanocyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
C27 H33 N5 O4 S
NDVQUNZCNAMROD-RZUBCFFCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A, C, D, F, G, I, J, L
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6Z3Kd: 90 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.196 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.643α = 90.00
b = 94.643β = 90.00
c = 368.582γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomERC-2012-StG-311460

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references