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 
  • R-Value Observed: 0.225 

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:  
    3HA6, 3HA8

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 6A268Homo sapiensMutation(s): 0 
Gene Names: AIKARK1AURAAURKABTAKSTK15STK6AIRK1AYK1IAK1
EC: 2.7.11.1
Find proteins for O14965 (Homo sapiens)
Explore O14965 
Go to UniProtKB:  O14965
NIH Common Fund Data Resources
PHAROS  O14965
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Targeting protein for Xklp2B44Homo sapiensMutation(s): 0 
Gene Names: C20orf1C20orf2DIL2HCA519TPX2
Find proteins for Q9ULW0 (Homo sapiens)
Explore Q9ULW0 
Go to UniProtKB:  Q9ULW0
NIH Common Fund Data Resources
PHAROS  Q9ULW0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2JZ
Query on 2JZ

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
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2JZIC50 :  2100   nM  PDBBind
2JZIC50:  2100   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.464α = 90
b = 86.464β = 90
c = 143.345γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance