4W9F

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 

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:  

  • 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: 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
3JU
Query on 3JU

Download SDF File 
Download CCD File 
C, F, I, L
(4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide
C22 H29 N3 O3 S
BULPVMQBJAMSRN-MSOLQXFVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3JUKd: 3270 nM (99) BINDINGDB
3JUKd: 3270 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.680α = 90.00
b = 92.680β = 90.00
c = 364.020γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata reduction
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
Marie Sklodowska-Curie ActionsEC PIEF-GA-2010-275683

Revision History 

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