3HA8

THE COMPLEX STRUCTURE OF THE MAP KINASE P38/Compound 14b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 

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
Mitogen-activated protein kinase 14
A
379Homo sapiensMutation(s): 0 
Gene Names: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A)
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Go to Gene View: MAPK14
Go to UniProtKB:  Q16539
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5JZ
Query on 5JZ

Download SDF File 
Download CCD File 
A
N~2~-{4-[6-(3,4-dihydroquinolin-1(2H)-ylcarbonyl)-1H-benzimidazol-1-yl]-6-ethoxy-1,3,5-triazin-2-yl}-3-(2,2-dimethyl-4H-1,3-benzodioxin-6-yl)-N-methyl-L-alaninamide
C36 H38 N8 O5
IIOQBYZRVQSNSJ-MHZLTWQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5JZEC50: <8 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.222α = 90.00
b = 87.934β = 90.00
c = 121.501γ = 90.00
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: Advisory, Refinement description, Version format compliance