4BKT

von Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions?

Dias, D.M.Van Molle, I.Baud, M.G.J.Galdeano, C.Geraldes, C.F.G.C.Ciulli, A.

(2014) ACS Med Chem Lett 5: 23

  • DOI: 10.1021/ml400296c
  • Primary Citation of Related Structures:  
    4BKS, 4BKT

  • PubMed Abstract: 
  • Modulation of protein-protein interactions (PPIs) with small molecules has been hampered by a lack of lucid methods capable of reliably identifying high-quality hits. In fragment screening, the low ligand efficiencies associated with PPI target sites ...

    Modulation of protein-protein interactions (PPIs) with small molecules has been hampered by a lack of lucid methods capable of reliably identifying high-quality hits. In fragment screening, the low ligand efficiencies associated with PPI target sites pose significant challenges to fragment binding detection. Here, we investigate the requirements for ligand-based NMR techniques to detect rule-of-three compliant fragments that form part of known high-affinity inhibitors of the PPI between the von Hippel-Lindau protein and the alpha subunit of hypoxia-inducible factor 1 (pVHL:HIF-1α). Careful triaging allowed rescuing weak but specific binding of fragments that would otherwise escape detection at this PPI. Further structural information provided by saturation transfer difference (STD) group epitope mapping, protein-based NMR, competitive isothermal titration calorimetry (ITC), and X-ray crystallography confirmed the binding mode of the rescued fragments. Our findings have important implications for PPI druggability assessment by fragment screening as they reveal an accessible threshold for fragment detection and validation.


    Organizational Affiliation

    Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2ADGJ104Homo 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
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  • Reference Sequence
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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
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  • Reference Sequence
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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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QD0
Query on QD0

Download CCD File 
C, F, I, L
(2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide
C12 H17 N3 O4
RKIBNEDMQYMQFM-SCZZXKLOSA-N
 Ligand Interaction
ARG
Query on ARG

Download CCD File 
I
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
GLU
Query on GLU

Download CCD File 
F
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A,D,G,JL-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QD0Kd:  240000   nM  Binding MOAD
QD0Kd:  240000   nM  BindingDB
QD0Kd :  240000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.18α = 90
b = 93.18β = 90
c = 364.5γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
BUSTERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2014-01-29
    Changes: Database references
  • Version 1.2: 2017-07-12
    Changes: Derived calculations