6R49

Aurora-A in complex with shape-diverse fragment 39


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.209 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Construction of a Shape-Diverse Fragment Set: Design, Synthesis and Screen against Aurora-A Kinase.

Zhang, R.McIntyre, P.J.Collins, P.M.Foley, D.J.Arter, C.von Delft, F.Bayliss, R.Warriner, S.Nelson, A.

(2019) Chemistry 25: 6831-6839

  • DOI: 10.1002/chem.201900815
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Historically, chemists have explored chemical space in a highly uneven and unsystematic manner. As an example, the shape diversity of existing fragment sets does not generally reflect that of all theoretically possible fragments. To assess experiment ...

    Historically, chemists have explored chemical space in a highly uneven and unsystematic manner. As an example, the shape diversity of existing fragment sets does not generally reflect that of all theoretically possible fragments. To assess experimentally the added value of increased three dimensionality, a shape-diverse fragment set was designed and collated. The set was assembled by both using commercially available fragments and harnessing unified synthetic approaches to sp 3 -rich molecular scaffolds. The resulting set of 80 fragments was highly three-dimensional, and its shape diversity was significantly enriched by twenty synthesised fragments. The fragment set was screened by high-throughput protein crystallography against Aurora-A kinase, revealing four hits that targeted the binding site of allosteric regulators. In the longer term, it is envisaged that the fragment set could be screened against a range of functionally diverse proteins, allowing the added value of more shape-diverse screening collections to be more fully assessed.


    Organizational Affiliation

    School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Department of Biochemistry, University of Johannesburg, Aukland Park, 2006, South Africa.,Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.,Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.,Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 9HN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aurora kinase A
A
285Homo sapiensMutation(s): 2 
Gene Names: AURKA (AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6)
EC: 2.7.11.1
Find proteins for O14965 (Homo sapiens)
Go to Gene View: AURKA
Go to UniProtKB:  O14965
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
JSB
Query on JSB

Download SDF File 
Download CCD File 
A
(1~{S},10~{S})-12-cyclopropyl-1-oxidanyl-10-propan-2-yl-9,12-diazatricyclo[8.2.1.0^{2,7}]trideca-2(7),3,5-trien-11-one
C17 H22 N2 O2
JXXKUMYBOLYKNF-IRXDYDNUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.209 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.192 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 82.272α = 90.00
b = 82.272β = 90.00
c = 174.043γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/K016903

Revision History 

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-22
    Type: Data collection, Database references
  • Version 1.2: 2019-07-10
    Type: Data collection