5M4E

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: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.6b01478
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Libraries of nonpurified resorcinol amide derivatives were screened by surface plasmon resonance (SPR) to determine the binding dissociation constant (off-rate, k <sub>d </sub>) for compounds binding to the pyruvate dehydrogenase kinase (PDHK) enzyme ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heat shock protein HSP 90-alpha
A
252Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1 (HSP90A, HSPC1, HSPCA)
Find proteins for P07900 (Homo sapiens)
Go to Gene View: HSP90AA1
Go to UniProtKB:  P07900
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7F9
Query on 7F9

Download SDF File 
Download CCD File 
A
~{N}-[2-(ethylamino)-2-oxidanylidene-ethyl]-~{N}-(4-methoxyphenyl)-2,4-bis(oxidanyl)benzamide
C18 H20 N2 O5
YRTAPVLIGYRBPY-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.163 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 65.388α = 90.00
b = 89.060β = 90.00
c = 99.505γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
REFMACrefinement
d*TREKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-10-18 
  • Released Date: 2017-02-22 
  • Deposition Author(s): Baker, L.M.

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references