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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 6268Homo sapiensMutation(s): 0 
Gene Names: AIKARK1AURAAURKABTAKSTK15STK6
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14965 (Homo sapiens)
Explore O14965 
Go to UniProtKB:  O14965
PHAROS:  O14965
GTEx:  ENSG00000087586 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14965
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Targeting protein for Xklp244Homo sapiensMutation(s): 0 
Gene Names: C20orf1C20orf2DIL2HCA519TPX2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULW0 (Homo sapiens)
Explore Q9ULW0 
Go to UniProtKB:  Q9ULW0
PHAROS:  Q9ULW0
GTEx:  ENSG00000088325 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULW0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2JZ
Query on 2JZ

Download Ideal Coordinates CCD File 
C [auth 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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
2JZ PDBBind:  3HA6 IC50: 2100 (nM) from 1 assay(s)
Binding MOAD:  3HA6 IC50: 2100 (nM) from 1 assay(s)
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

Revision History  (Full details and data files)

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