3ZRC

pVHL54-213-EloB-EloC complex (4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.350 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Targeting the Von Hippel-Lindau E3 Ubiquitin Ligase Using Small Molecules to Disrupt the Vhl/Hif-1Alpha Interaction

Buckley, D.L.Van Molle, I.Gareiss, P.C.Tae, H.S.Michel, J.Noblin, D.J.Jorgensen, W.L.Ciulli, A.Crews, C.M.

(2012) J.Am.Chem.Soc. 134: 4465

  • DOI: 10.1021/ja209924v
  • Primary Citation of Related Structures:  3ZRF

  • PubMed Abstract: 
  • E3 ubiquitin ligases, which bind protein targets, leading to their ubiquitination and subsequent degradation, are attractive drug targets due to their exquisite substrate specificity. However, the development of small-molecule inhibitors has proven e ...

    E3 ubiquitin ligases, which bind protein targets, leading to their ubiquitination and subsequent degradation, are attractive drug targets due to their exquisite substrate specificity. However, the development of small-molecule inhibitors has proven extraordinarily challenging as modulation of E3 ligase activities requires the targeting of protein-protein interactions. Using rational design, we have generated the first small molecule targeting the von Hippel-Lindau protein (VHL), the substrate recognition subunit of an E3 ligase, and an important target in cancer, chronic anemia, and ischemia. We have also obtained the crystal structure of VHL bound to our most potent inhibitor, confirming that the compound mimics the binding mode of the transcription factor HIF-1α, a substrate of VHL. These results have the potential to guide future development of improved lead compounds as therapeutics for the treatment of chronic anemia and ischemia.


    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
A, D, G, J
118Homo sapiensGene Names: TCEB2
Find proteins for Q15370 (Homo sapiens)
Go to UniProtKB:  Q15370
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
B, E, H, K
97Homo sapiensGene Names: TCEB1
Find proteins for Q15369 (Homo sapiens)
Go to UniProtKB:  Q15369
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
C, F, I, L
163Homo sapiensGene 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
L8B
Query on L8B

Download SDF File 
Download CCD File 
C, F, I, L
(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-N-[4-(1,3-OXAZOL-5-YL)BENZYL]-L-PROLINAMIDE
C21 H22 N4 O5
HFCLIEBJTGJKSV-AEFFLSMTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L8BIC50: 4100 nM (100) BINDINGDB
L8BKd: 5300 - 5500 nM (98) BINDINGDB
L8BKd: 5400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.350 
  • R-Value Work: 0.242 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.741α = 90.00
b = 93.741β = 90.00
c = 363.184γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Other