6G4Y

Crystal structure of murine NF-kappaB inducing kinase (NIK) in complex with compound 1a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


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: Map3k14Nik
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ELZ
Query on ELZ

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
10-[2-[(3~{R})-1-methyl-3-oxidanyl-2-oxidanylidene-pyrrolidin-3-yl]ethynyl]-~{N}3-(oxan-4-yl)-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepine-2,3-dicarboxamide
C25 H27 N5 O6
ZGTZKIXFBFZCBL-VWLOTQADSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B],
G [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ELZ BindingDB:  6G4Y Ki: 0.73 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.829α = 90
b = 143.829β = 90
c = 45.614γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



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