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 

wwPDB Validation 3D Report Full Report


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:  

  • PubMed Abstract: 
  • NF-κB-inducing kinase (NIK) is a protein kinase central to the non-canonical NF-κB pathway downstream from multiple TNF receptor family members, including BAFF, which have been associated with B cell survival and maturation, dendritic cell activation ...

    NF-κB-inducing kinase (NIK) is a protein kinase central to the non-canonical NF-κB pathway downstream from multiple TNF receptor family members, including BAFF, which have been associated with B cell survival and maturation, dendritic cell activation, secondary lymphoid organ development, and bone metabolism. We report herein the discovery of a lead chemical series of NIK-inhibitors that was 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase kinase kinase 14
A, B
349Mus musculusMutation(s): 0 
Gene Names: Map3k14 (Nik)
EC: 2.7.11.25
Find proteins for Q9WUL6 (Mus musculus)
Go to UniProtKB:  Q9WUL6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ELW
Query on ELW

Download SDF File 
Download CCD File 
A, 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 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 144.830α = 90.00
b = 144.830β = 90.00
c = 46.530γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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