5M4K

Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase.

Brough, P.A.Baker, L.Bedford, S.Brown, K.Chavda, S.Chell, V.D'Alessandro, J.Davies, N.G.Davis, B.Le Strat, L.Macias, A.T.Maddox, D.Mahon, P.C.Massey, A.J.Matassova, N.McKenna, S.Meissner, J.W.Moore, J.D.Murray, J.B.Northfield, C.J.Parry, C.Parsons, R.Roughley, S.D.Shaw, T.Simmonite, H.Stokes, S.Surgenor, A.Stefaniak, E.Robertson, A.Wang, Y.Webb, P.Whitehead, N.Wood, M.

(2017) J Med Chem 60: 2271-2286

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01478
  • Primary Citation of Related Structures:  
    5M4E, 5M4H, 5M4K, 5M4M, 5M4N, 5M4P

  • PubMed Abstract: 

    Libraries of nonpurified resorcinol amide derivatives were screened by surface plasmon resonance (SPR) to determine the binding dissociation constant (off-rate, k d ) for compounds binding to the pyruvate dehydrogenase kinase (PDHK) enzyme. Parallel off-rate measurements against HSP90 and application of structure-based drug design enabled rapid hit to lead progression in a program to identify pan-isoform ATP-competitive inhibitors of PDHK. Lead optimization identified selective sub-100-nM inhibitors of the enzyme which significantly reduced phosphorylation of the E1α subunit in the PC3 cancer cell line in vitro.


  • Organizational Affiliation

    Vernalis (R&D) Ltd. , Granta Park, Great Abington, Cambridge CB21 6GB, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial408Homo sapiensMutation(s): 0 
Gene Names: PDK2PDHK2
EC: 2.7.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15119 (Homo sapiens)
Explore Q15119 
Go to UniProtKB:  Q15119
PHAROS:  Q15119
GTEx:  ENSG00000005882 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15119
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TF3
Query on TF3

Download Ideal Coordinates CCD File 
B [auth A]N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE
C20 H25 Cl N2 O2
DFXJYVQAAFOZDP-UHFFFAOYSA-N
7F9
Query on 7F9

Download Ideal Coordinates CCD File 
C [auth A]~{N}-[2-(ethylamino)-2-oxidanylidene-ethyl]-~{N}-(4-methoxyphenyl)-2,4-bis(oxidanyl)benzamide
C18 H20 N2 O5
YRTAPVLIGYRBPY-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
7F9 BindingDB:  5M4K Ki: 2170 (nM) from 1 assay(s)
IC50: 4460 (nM) from 1 assay(s)
TF3 BindingDB:  5M4K IC50: 2000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.092α = 90
b = 108.092β = 90
c = 84.441γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description