6FMJ

pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-Acetamidopropanethioyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl) benzyl)pyrrolidine-2-carboxamide (ligand 3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Thioamide substitution to probe the hydroxyproline recognition of VHL ligands.

Soares, P.Lucas, X.Ciulli, A.

(2018) Bioorg. Med. Chem. 26: 2992-2995

  • DOI: 10.1016/j.bmc.2018.03.034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thioamide substitution influences hydrogen bond and n → π <sup>∗ </sup> interactions involved in the conformational stability of protein secondary structures and oligopeptides. Hydroxyproline is the key recognition element of small molecules targetin ...

    Thioamide substitution influences hydrogen bond and n → π interactions involved in the conformational stability of protein secondary structures and oligopeptides. Hydroxyproline is the key recognition element of small molecules targeting the von Hippel-Lindau (VHL) E3 ligase, which are of interest as probes of hypoxia signaling and ligands for PROTAC conjugation. We hypothesized that VHL ligands could be a privileged model system to evaluate the contribution of these interactions to protein:ligand complex formation. Herein we report the synthesis of VHL ligands bearing thioamide substitutions at the central hydroxyproline moiety, and characterize their binding by fluorescence polarization, isothermal titration calorimetry, X-ray crystallography and molecular modeling. In spite of a conserved binding mode, the substitution pattern had a pronounced impact on the ligand affinities. Together the results underscore the role of hydrogen bond and n → π interactions in fine tuning hydroxyproline recognition by VHL.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK. Electronic address: a.ciulli@dundee.ac.uk.,Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongin-B
A, D, G, J
104Homo sapiensMutation(s): 0 
Gene Names: ELOB (TCEB2)
Find proteins for Q15370 (Homo sapiens)
Go to Gene View: ELOB
Go to UniProtKB:  Q15370
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Elongin-C
B, E, H, K
97Homo sapiensMutation(s): 0 
Gene Names: ELOC (TCEB1)
Find proteins for Q15369 (Homo sapiens)
Go to Gene View: ELOC
Go to UniProtKB:  Q15369
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
von Hippel-Lindau disease tumor suppressor
C, F, I, L
153Homo sapiensMutation(s): 0 
Gene 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
DV5
Query on DV5

Download SDF File 
Download CCD File 
C, F, I, L
(2~{S},4~{R})-1-[(2~{S})-2-acetamidopropanethioyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
C21 H26 N4 O3 S2
WHYNNQMYHZONCV-VHSSKADRSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A, C, D, F, G, I, J, L
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DV5Kd: 760 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.518α = 90.00
b = 93.518β = 90.00
c = 364.314γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited KingdomERC-2012-StG-311460 DrugE3CRLs

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Database references
  • Version 1.2: 2018-06-20
    Type: Data collection, Database references, Derived calculations