3ZTD

pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Dissecting Fragment-Based Lead Discovery at the Von Hippel-Lindau Protein:Hypoxia Inducible Factor 1Alpha Protein-Protein Interface.

Van Molle, I.Thomann, A.Buckley, D.L.So, E.C.Lang, S.Crews, C.M.Ciulli, A.

(2012) Chem.Biol. 19: 1300

  • DOI: 10.1016/j.chembiol.2012.08.015
  • Primary Citation of Related Structures:  4AJY, 4AWJ, 3ZTC

  • PubMed Abstract: 
  • Fragment screening is widely used to identify attractive starting points for drug design. However, its potential and limitations to assess the tractability of often challenging protein:protein interfaces have been underexplored. Here, we address this ...

    Fragment screening is widely used to identify attractive starting points for drug design. However, its potential and limitations to assess the tractability of often challenging protein:protein interfaces have been underexplored. Here, we address this question by means of a systematic deconstruction of lead-like inhibitors of the pVHL:HIF-1α interaction into their component fragments. Using biophysical techniques commonly employed for screening, we could only detect binding of fragments that violate the Rule of Three, are more complex than those typically screened against classical druggable targets, and occupy two adjacent binding subsites at the interface rather than just one. Analyses based on ligand and group lipophilicity efficiency of anchored fragments were applied to dissect the individual subsites and probe for binding hot spots. The implications of our findings for targeting protein interfaces by fragment-based approaches are discussed.


    Organizational Affiliation

    Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.




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
162Homo 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
ZTD
Query on ZTD

Download SDF File 
Download CCD File 
C, F, I, L
METHYL 4-[({(4R)-4-HYDROXY-1-[(3-METHYLISOXAZOL-5-YL)ACETYL]-L-PROLYL}AMINO)METHYL]BENZOATE
C20 H23 N3 O6
HMFSOBWOOWBCBL-WBVHZDCISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZTDKd: 96200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.224 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.081α = 90.00
b = 94.081β = 90.00
c = 366.494γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Database references, Structure summary