6MYN

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

• PDB DOI: https://doi.org/10.2210/pdb6MYN/pdb

• Classification: TRANSFERASE/TRANSFERASE Inhibitor
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2018-11-01 Released: 2019-08-07 
• Deposition Author(s): Harris, S.F., Smith, M., Barker, J.

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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 

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

• PubMed: 31531194 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00658
• Primary Citation of Related Structures:  
  5W5Q, 6MYN


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.21 kDa 
• Atom Count: 5,280 
• Modelled Residue Count: 650 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 14	A, B	347	Mus musculus	Mutation(s): 0  Gene Names: Map3k14, Nik EC: 2.7.11.25
UniProt
Find proteins for Q9WUL6 (Mus musculus) Explore Q9WUL6  Go to UniProtKB:  Q9WUL6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K6Y (Subject of Investigation/LOI)	E [auth A], I [auth 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
SO4	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
K6Y	BindingDB:  6MYN	Ki: min: 8, max: 14 (nM) from 2 assay(s)

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 = 143.22	α = 90
b = 143.22	β = 90
c = 46.41	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Harris, S.F., Smith, M., Barker, J.

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
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references