4BI1

Scaffold Focused Virtual Screening: Prospective Application to the Discovery of TTK Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Scaffold-Focused Virtual Screening: Prospective Application to the Discovery of Ttk Inhibitors.

Langdon, S.R.Westwood, I.M.Van Montfort, R.L.M.Brown, N.Blagg, J.

(2013) J.Chem.Inf.Model 53: 1100

  • DOI: 10.1021/ci400100c
  • Primary Citation of Related Structures:  4BHZ, 4BI0, 4BI2

  • PubMed Abstract: 
  • We describe and apply a scaffold-focused virtual screen based upon scaffold trees to the mitotic kinase TTK (MPS1). Using level 1 of the scaffold tree, we perform both 2D and 3D similarity searches between a query scaffold and a level 1 scaffold libr ...

    We describe and apply a scaffold-focused virtual screen based upon scaffold trees to the mitotic kinase TTK (MPS1). Using level 1 of the scaffold tree, we perform both 2D and 3D similarity searches between a query scaffold and a level 1 scaffold library derived from a 2 million compound library; 98 compounds from 27 unique top-ranked level 1 scaffolds are selected for biochemical screening. We show that this scaffold-focused virtual screen prospectively identifies eight confirmed active compounds that are structurally differentiated from the query compound. In comparison, 100 compounds were selected for biochemical screening using a virtual screen based upon whole molecule similarity resulting in 12 confirmed active compounds that are structurally similar to the query compound. We elucidated the binding mode for four of the eight confirmed scaffold hops to TTK by determining their protein-ligand crystal structures; each represents a ligand-efficient scaffold for inhibitor design.


    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, Surrey, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DUAL SPECIFICITY PROTEIN KINASE TTK
A
313Homo sapiensGene Names: TTK (MPS1, MPS1L1)
EC: 2.7.12.1
Find proteins for P33981 (Homo sapiens)
Go to Gene View: TTK
Go to UniProtKB:  P33981
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
7PE
Query on 7PE

Download SDF File 
Download CCD File 
A
2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
POLYETHYLENE GLYCOL FRAGMENT
C14 H30 O7
UKXKPKBTMYNOFS-UHFFFAOYSA-N
 Ligand Interaction
ZO6
Query on ZO6

Download SDF File 
Download CCD File 
A
thieno[3,2-c][2,6]naphthyridine
C10 H6 N2 S
NKBQKUDYRMOAKU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZO6IC50: 69100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.188 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 70.910α = 90.00
b = 111.820β = 90.00
c = 113.570γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references