6G4Z

Crystal structure of murine NF-kappaB inducing kinase (NIK) in complex with compound 2f

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Scaffold-Hopping Approach To Discover Potent, Selective, and Efficacious Inhibitors of NF-kappa B Inducing Kinase.

Blaquiere, N., Castanedo, G.M., Burch, J.D., Berezhkovskiy, L.M., Brightbill, H., Brown, S., Chan, C., Chiang, P.C., Crawford, J.J., Dong, T., Fan, P., Feng, J., Ghilardi, N., Godemann, R., Gogol, E., Grabbe, A., Hole, A.J., Hu, B., Hymowitz, S.G., Alaoui Ismaili, M.H., Le, H., Lee, P., Lee, W., Lin, X., Liu, N., McEwan, P.A., McKenzie, B., Silvestre, H.L., Suto, E., Sujatha-Bhaskar, S., Wu, G., Wu, L.C., Zhang, Y., Zhong, Z., Staben, S.T.

(2018) J Med Chem 61: 6801-6813

  • DOI: 10.1021/acs.jmedchem.8b00678
  • Primary Citation of Related Structures:  
    6G4Y, 6G4Z

  • PubMed Abstract: 

    • NF-κB-inducing kinase (NIK) is a protein kinase central to the noncanonical NF-κB pathway downstream from multiple TNF receptor family members, including BAFF, which has been associated with B cell survival and maturation, dendritic cell activation, secondary lymphoid organ development, and bone metabolism ...

    NF-κB-inducing kinase (NIK) is a protein kinase central to the noncanonical NF-κB pathway downstream from multiple TNF receptor family members, including BAFF, which has been associated with B cell survival and maturation, dendritic cell activation, secondary lymphoid organ development, and bone metabolism. We report herein the discovery of lead chemical series of NIK inhibitors that were identified through a scaffold-hopping strategy using structure-based design. Electronic and steric properties of lead compounds were modified to address glutathione conjugation and amide hydrolysis. These highly potent compounds exhibited selective inhibition of LTβR-dependent p52 translocation and transcription of NF-κB2 related genes. Compound 4f is shown to have a favorable pharmacokinetic profile across species and to inhibit BAFF-induced B cell survival in vitro and reduce splenic marginal zone B cells in vivo.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 14A, B349Mus musculusMutation(s): 0 
Gene Names: Map3k14, Nik
EC: 2.7.11.25
UniProt
Find proteins for Q9WUL6 (Mus musculus)
Explore Q9WUL6 
Go to UniProtKB:  Q9WUL6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WUL6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ELW
Query on ELW
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		5-fluoranyl-1-[4-[2-[(3~{R})-1-methyl-3-oxidanyl-2-oxidanylidene-pyrrol-3-yl]ethynyl]pyridin-2-yl]indazole-3-carboxamide
C20 H14 F N5 O3
ZZMZSZVGWQGKCR-FQEVSTJZSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.83α = 90
b = 144.83β = 90
c = 46.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-22
    Changes: Data collection, Database references, Structure summary