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: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report



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:  
    4IDT, 4IDV

  • 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 scaffo ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 14 A, B, C, D356Homo sapiensMutation(s): 0 
Gene Names: MAP3K14, NIK
EC: 2.7.11.25
Find proteins for Q99558 (Homo sapiens)
Explore Q99558 
Go to UniProtKB:  Q99558
NIH Common Fund Data Resources
PHAROS:  Q99558
GTEx:  ENSG00000006062
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13V
Query on 13V
Download Ideal Coordinates 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 :  40   nM  PDBBind
13VIC50:  20   nM  BindingDB
13VIC50:  40   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.378α = 90
b = 146.014β = 90
c = 254.701γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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