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 

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Ligand Structure Quality Assessment 


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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase 6268Homo sapiensMutation(s): 0 
Gene Names: AIK, ARK1, AURA, AURKA, BTAK, STK15, STK6, AIRK1, AYK1, IAK1
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14965
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Targeting protein for Xklp244Homo sapiensMutation(s): 0 
Gene Names: C20orf1, C20orf2, DIL2, HCA519, TPX2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULW0 (Homo sapiens)
Explore Q9ULW0 
Go to UniProtKB:  Q9ULW0
PHAROS:  Q9ULW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULW0
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 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		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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

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Ligand Structure Quality Assessment 


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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