6GFZ

pVHL:EloB:EloC in complex with modified VH032 containing (3S,4S)-3-fluoro-4-hydroxyproline (ligand 14b)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation.

Testa, A.Lucas, X.Castro, G.V.Chan, K.H.Wright, J.E.Runcie, A.C.Gadd, M.S.Harrison, W.T.A.Ko, E.J.Fletcher, D.Ciulli, A.

(2018) J Am Chem Soc 140: 9299-9313

  • DOI: https://doi.org/10.1021/jacs.8b05807
  • Primary Citation of Related Structures:  
    6GFX, 6GFY, 6GFZ

  • PubMed Abstract: 

    Hydroxylation and fluorination of proline alters the pyrrolidine ring pucker and the trans:cis amide bond ratio in a stereochemistry-dependent fashion, affecting molecular recognition of proline-containing molecules by biological systems. While hydroxyprolines and fluoroprolines are common motifs in medicinal and biological chemistry, the synthesis and molecular properties of prolines containing both modifications, i.e., fluoro-hydroxyprolines, have not been described. Here we present a practical and facile synthesis of all four diastereoisomers of 3-fluoro-4-hydroxyprolines (F-Hyps), starting from readily available 4-oxo-l-proline derivatives. Small-molecule X-ray crystallography, NMR spectroscopy, and quantum mechanical calculations are consistent with fluorination at C 3 having negligible effects on the hydrogen bond donor capacity of the C 4 hydroxyl, but inverting the natural preference of Hyp from C 4 -exo to C 4 -endo pucker. In spite of this, F-Hyps still bind to the von Hippel-Lindau (VHL) E3 ligase, which naturally recognizes C 4 -exo Hyp in a stereoselective fashion. Co-crystal structures and electrostatic potential calculations support and rationalize the observed preferential recognition for (3 R,4 S)-F-Hyp over the corresponding (3 S,4 S) epimer by VHL. We show that (3 R,4 S)-F-Hyp provides bioisosteric Hyp substitution in both hypoxia-inducible factor 1 alpha (HIF-1α) substrate peptides and peptidomimetic ligands that form part of PROTAC (proteolysis targeting chimera) conjugates for targeted protein degradation. Despite a weakened affinity, Hyp substitution with (3 S,4 S)-F-Hyp within the PROTAC MZ1 led to Brd4-selective cellular degradation at concentrations >100-fold lower than the binary K d for VHL. We anticipate that the disclosed chemistry of 3-fluoro-4-hydroxyprolines and their application as VHL ligands for targeted protein degradation will be of wide interest to medicinal organic chemists, chemical biologists, and drug discoverers alike.


  • Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B
A, D, G, J
104Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
PHAROS:  Q15370
GTEx:  ENSG00000103363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15370
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-C
B, E, H, K
97Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15369
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressor
C, F, I, L
162Homo sapiensMutation(s): 0 
Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens)
Explore P40337 
Go to UniProtKB:  P40337
PHAROS:  P40337
GTEx:  ENSG00000134086 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40337
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EXE (Subject of Investigation/LOI)
Query on EXE

Download Ideal Coordinates CCD File 
M [auth C],
N [auth F],
O [auth I],
P [auth L]
(2~{R},3~{S},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
C24 H31 F N4 O4 S
MNNVXLLCYGGFOQ-YOUFYPILSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CAS
Query on CAS
A, D, G, J
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.609α = 90
b = 93.609β = 90
c = 364.511γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilERC-2012-StG-311460 DrugE3CRLs

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description