4AJY

von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


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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, 3ZTC, 3ZTD, 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 question by means of a systematic deconstruction of lead-like inhibitors of the pVHL:HIF-1α interaction into their component fragments ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2 B118Homo sapiensMutation(s): 0 
Gene Names: ELOB, TCEB2
Find proteins for Q15370 (Homo sapiens)
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Go to UniProtKB:  Q15370
NIH Common Fund Data Resources
PHAROS:  Q15370
GTEx:  ENSG00000103363
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1 C97Homo sapiensMutation(s): 0 
Gene Names: ELOC, TCEB1
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
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PHAROS:  Q15369
GTEx:  ENSG00000154582
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOXIA-INDUCIBLE FACTOR 1-ALPHA H19Homo sapiensMutation(s): 2 
Gene Names: HIF1A, BHLHE78, MOP1, PASD8
Find proteins for Q16665 (Homo sapiens)
Explore Q16665 
Go to UniProtKB:  Q16665
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PHAROS:  Q16665
GTEx:  ENSG00000100644
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR V163Homo sapiensMutation(s): 0 
Gene Names: VHL
Find proteins for P40337 (Homo sapiens)
Explore P40337 
Go to UniProtKB:  P40337
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PHAROS:  P40337
GTEx:  ENSG00000134086
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
V
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP		HL-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.232α = 90
b = 59.232β = 90
c = 244.038γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release