4W9E

pVHL:EloB:EloC in complex with (2S,4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(thiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities.

Galdeano, C.Gadd, M.S.Soares, P.Scaffidi, S.Van Molle, I.Birced, I.Hewitt, S.Dias, D.M.Ciulli, A.

(2014) J Med Chem 57: 8657-8663

  • DOI: 10.1021/jm5011258
  • Primary Citation of Related Structures:  
    4W9F, 4W9G, 4W9H, 4W9I, 4W9J, 4W9K, 4W9L, 4W9C, 4W9D, 4W9E

  • PubMed Abstract: 
  • E3 ubiquitin ligases are attractive targets in the ubiquitin-proteasome system, however, the development of small-molecule ligands has been rewarded with limited success. The von Hippel-Lindau protein (pVHL) is the substrate recognition subunit of th ...

    E3 ubiquitin ligases are attractive targets in the ubiquitin-proteasome system, however, the development of small-molecule ligands has been rewarded with limited success. The von Hippel-Lindau protein (pVHL) is the substrate recognition subunit of the VHL E3 ligase that targets HIF-1α for degradation. We recently reported inhibitors of the pVHL:HIF-1α interaction, however they exhibited moderate potency. Herein, we report the design and optimization, guided by X-ray crystal structures, of a ligand series with nanomolar binding affinities.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee , Dow Street, Dundee, DD1 5EH, Scotland, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor B polypeptide 2ADGJ104Homo sapiensMutation(s): 0 
Gene Names: TCEB2ELOB
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
NIH Common Fund Data Resources
PHAROS  Q15370
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor B polypeptide 1BEHK97Homo sapiensMutation(s): 0 
Gene Names: TCEB1ELOC
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
NIH Common Fund Data Resources
PHAROS  Q15369
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Von Hippel-Lindau disease tumor suppressorCFIL162Homo sapiensMutation(s): 0 
Gene Names: VHL
Find proteins for P40337 (Homo sapiens)
Explore P40337 
Go to UniProtKB:  P40337
NIH Common Fund Data Resources
PHAROS  P40337
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3JT
Query on 3JT

Download CCD File 
C, F, I, L
(4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide
C21 H27 N3 O3 S
ZFCSIIZHOAAIJZ-SJORKVTESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A,D,G,JL-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3JTKd:  7090   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.097α = 90
b = 93.097β = 90
c = 364.436γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
XSCALEdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilERC-2012-StG-311460
Biotechnology and Biological Sciences Research CouncilUnited KingdomBBSRC BB/G023123/1
Marie Sklodowska-Curie ActionsEC PIEF-GA-2012-328030

Revision History 

  • Version 1.0: 2014-09-10
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references