3HA6

Crystal structure of aurora A in complex with TPX2 and compound 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design, synthesis and selection of DNA-encoded small-molecule libraries.

Clark, M.A.Acharya, R.A.Arico-Muendel, C.C.Belyanskaya, S.L.Benjamin, D.R.Carlson, N.R.Centrella, P.A.Chiu, C.H.Creaser, S.P.Cuozzo, J.W.Davie, C.P.Ding, Y.Franklin, G.J.Franzen, K.D.Gefter, M.L.Hale, S.P.Hansen, N.J.Israel, D.I.Jiang, J.Kavarana, M.J.Kelley, M.S.Kollmann, C.S.Li, F.Lind, K.Mataruse, S.Medeiros, P.F.Messer, J.A.Myers, P.O'Keefe, H.Oliff, M.C.Rise, C.E.Satz, A.L.Skinner, S.R.Svendsen, J.L.Tang, L.van Vloten, K.Wagner, R.W.Yao, G.Zhao, B.Morgan, B.A.

(2009) Nat.Chem.Biol. 5: 647-654

  • DOI: 10.1038/nchembio.211
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Biochemical combinatorial techniques such as phage display, RNA display and oligonucleotide aptamers have proven to be reliable methods for generation of ligands to protein targets. Adapting these techniques to small synthetic molecules has been a lo ...

    Biochemical combinatorial techniques such as phage display, RNA display and oligonucleotide aptamers have proven to be reliable methods for generation of ligands to protein targets. Adapting these techniques to small synthetic molecules has been a long-sought goal. We report the synthesis and interrogation of an 800-million-member DNA-encoded library in which small molecules are covalently attached to an encoding oligonucleotide. The library was assembled by a combination of chemical and enzymatic synthesis, and interrogated by affinity selection. We describe methods for the selection and deconvolution of the chemical display library, and the discovery of inhibitors for two enzymes: Aurora A kinase and p38 MAP kinase.


    Organizational Affiliation

    Praecis Pharmaceuticals, Waltham, Massachusetts, USA




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase 6
A
268Homo sapiensMutation(s): 0 
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Targeting protein for Xklp2
B
44Homo sapiensMutation(s): 0 
Gene Names: TPX2 (C20orf1, C20orf2, DIL2, HCA519)
Find proteins for Q9ULW0 (Homo sapiens)
Go to Gene View: TPX2
Go to UniProtKB:  Q9ULW0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2JZ
Query on 2JZ

Download SDF File 
Download CCD File 
A
N~2~-(3,4-dimethoxyphenyl)-N~4~-[2-(2-fluorophenyl)ethyl]-N~6~-quinolin-6-yl-1,3,5-triazine-2,4,6-triamine
C28 H26 F N7 O2
FLCQZZIDGSESAD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2JZIC50: 2100 nM BINDINGMOAD
2JZIC50: 2100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.224 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.464α = 90.00
b = 86.464β = 90.00
c = 143.345γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-05-01 
  • Released Date: 2009-08-04 
  • Deposition Author(s): Zhao, B., Clark, M.A.

Revision History 

  • Version 1.0: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance