5FND

Dynamic Undocking and the Quasi-Bound State as tools for Drug Design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dynamic undocking and the quasi-bound state as tools for drug discovery.

Ruiz-Carmona, S.Schmidtke, P.Luque, F.J.Baker, L.Matassova, N.Davis, B.Roughley, S.Murray, J.Hubbard, R.Barril, X.

(2017) Nat Chem 9: 201-206

  • DOI: 10.1038/nchem.2660
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • There is a pressing need for new technologies that improve the efficacy and efficiency of drug discovery. Structure-based methods have contributed towards this goal but they focus on predicting the binding affinity of protein-ligand complexes, which ...

    There is a pressing need for new technologies that improve the efficacy and efficiency of drug discovery. Structure-based methods have contributed towards this goal but they focus on predicting the binding affinity of protein-ligand complexes, which is notoriously difficult. We adopt an alternative approach that evaluates structural, rather than thermodynamic, stability. As bioactive molecules present a static binding mode, we devised dynamic undocking (DUck), a fast computational method to calculate the work necessary to reach a quasi-bound state at which the ligand has just broken the most important native contact with the receptor. This non-equilibrium property is surprisingly effective in virtual screening because true ligands form more-resilient interactions than decoys. Notably, DUck is orthogonal to docking and other 'thermodynamic' methods. We demonstrate the potential of the docking-undocking combination in a fragment screening against the molecular chaperone and oncology target Hsp90, for which we obtain novel chemotypes and a hit rate that approaches 40%.


    Organizational Affiliation

    Vernalis (R&D) Ltd, Granta Park, Cambridge CB21 6GB, UK.,YSBL, University of York, Heslington, York YO10 5DD, UK.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.,Discngine, 33 rue du Fauburg Saint-Antoine, 75011 Paris, France.,Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEAT SHOCK PROTEIN, HSP90-ALPHA
A
236Homo 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IQ5
Query on IQ5

Download SDF File 
Download CCD File 
A
N-(2-AZANYL-6-METHYL-1,3-BENZOTHIAZOL-5-YL)ETHANAMIDE
C10 H11 N3 O S
DUWIACCTNKYBNV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IQ5Kd: 320000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.221 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 64.960α = 90.00
b = 88.412β = 90.00
c = 99.059γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SAINTdata reduction
SADABSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Database references
  • Version 1.2: 2019-11-06
    Type: Data collection, Other