6MYN

Crystal structure of murine NF-kappaB inducing kinase (NIK) bound to inhibitor R7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure Based Design of Potent Selective Inhibitors of Protein Kinase D1 (PKD1).

Feng, J.A.Lee, P.Alaoui, M.H.Barrett, K.Castanedo, G.Godemann, R.McEwan, P.Wang, X.Wu, P.Zhang, Y.Harris, S.F.Staben, S.T.

(2019) ACS Med Chem Lett 10: 1260-1265

  • DOI: 10.1021/acsmedchemlett.8b00658
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We previously disclosed a series of type I 1/2 inhibitors of NF-κB inducing kinase (NIK). Inhibition of NIK by these compounds was found to be strongly dependent on the inclusion and absolute stereochemistry of a propargyl tertiary alcohol as it form ...

    We previously disclosed a series of type I 1/2 inhibitors of NF-κB inducing kinase (NIK). Inhibition of NIK by these compounds was found to be strongly dependent on the inclusion and absolute stereochemistry of a propargyl tertiary alcohol as it forms critical hydrogen bonds (H-bonds) with NIK. We report that inhibition of protein kinase D1 (PKD1) by this class of compounds is not dependent on H-bond interactions of this tertiary alcohol. This feature was leveraged in the design of highly selective inhibitors of PKD1 that no longer inhibit NIK. A structure-based hypothesis based on the position and flexibility of the α-C-helix of PKD1 vs NIK is presented.


    Related Citations: 
    • Structure based design of potent selective inhibitors of protein kinase D1 (PKD1)
      Feng, J.W., Lee, P., Alaoui, M.H., Barrett, K., Castaneda, G.M., Godemann, R., McEwan, P., Wang, X., Wu, P., Zhang, Y., Harris, S.F., Staben, S.T.
      (2019) ACS Med Chem Lett --: --

    Organizational Affiliation

    Genentech, 1 DNA way, South San Francisco, California 94080, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase kinase kinase 14
A, B
347Mus musculusMutation(s): 0 
Gene Names: Map3k14Nik
EC: 2.7.11.25
Find proteins for Q9WUL6 (Mus musculus)
Go to UniProtKB:  Q9WUL6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K6Y
Query on K6Y

Download CCD File 
A, B
(5s,7s)-9-fluoro-10-[(3R)-3-hydroxy-3-(5-methyl-1,2-oxazol-3-yl)but-1-yn-1-yl]-N~3~-methyl-6,7-dihydro-5H-5,7-methanoimidazo[2,1-a][2]benzazepine-2,3-dicarboxamide
C24 H22 F N5 O4
GFVXWRXUSFUWQS-QWJLCTJOSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.187 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.22α = 90
b = 143.22β = 90
c = 46.41γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-02
    Changes: Data collection, Database references