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 
  • R-Value Observed: 0.229 

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:  
    3ZTC, 3ZTD, 4AJY, 4AWJ

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2ADGJ118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
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: ELOCTCEB1
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
ZTD
Query on ZTD

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 
  • R-Value Observed: 0.229 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.081α = 90
b = 94.081β = 90
c = 366.494γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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