4IDV

Crystal Structure of NIK with compound 4-{3-[2-amino-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl}-2-methylbut-3-yn-2-ol (13V)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Inhibiting NF-KB-inducing kinase (NIK): Discovery, structure-based design, synthesis, structure activity relationship, and co-crystal structures

Li, K.McGee, L.R.Fisher, B.Sudom, A.Liu, J.Rubenstein, S.M.Anwer, M.K.Cushing, T.D.Shin, Y.Ayres, M.Lee, F.Eksterowicz, J.Faulder, P.Waszkowycz, B.Plotnikova, O.Farrelly, E.Xiao, S.H.Chen, G.Wang, Z.

(2013) Bioorg.Med.Chem.Lett. 23: 1238-1244

  • DOI: 10.1016/j.bmcl.2013.01.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery, structure-based design, synthesis, and optimization of NIK inhibitors are described. Our work began with an HTS hit, imidazopyridinyl pyrimidinamine 1. We utilized homology modeling and conformational analysis to optimize the indole sc ...

    The discovery, structure-based design, synthesis, and optimization of NIK inhibitors are described. Our work began with an HTS hit, imidazopyridinyl pyrimidinamine 1. We utilized homology modeling and conformational analysis to optimize the indole scaffold leading to the discovery of novel and potent conformationally constrained inhibitors such as compounds 25 and 28. Compounds 25 and 31 were co-crystallized with NIK kinase domain to provide structural insights.


    Organizational Affiliation

    Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA. kli@amgen.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase kinase kinase 14
A, B, C, D
356Homo sapiensMutation(s): 0 
Gene Names: MAP3K14 (NIK)
EC: 2.7.11.25
Find proteins for Q99558 (Homo sapiens)
Go to Gene View: MAP3K14
Go to UniProtKB:  Q99558
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13V
Query on 13V

Download SDF File 
Download CCD File 
A, B, C, D
4-{3-[2-amino-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl}-2-methylbut-3-yn-2-ol
C20 H22 N4 O3
ZZIZLABGKZWVAW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
13VIC50: 20 - 40 nM (100) BINDINGDB
13VIC50: 40 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.378α = 90.00
b = 146.014β = 90.00
c = 254.701γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release