7SZR

NIK bound to inhibitor G02792917


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Filling a nick in NIK: Extending the half-life of a NIK inhibitor through structure-based drug design.

Crawford, J.J.Feng, J.Brightbill, H.D.Johnson, A.R.Wright, M.Kolesnikov, A.Lee, W.Castanedo, G.M.Do, S.Blaquiere, N.Staben, S.T.Chiang, P.C.Fan, P.W.Baumgardner, M.Wong, S.Godemann, R.Grabbe, A.Wiegel, C.Sujatha-Bhaskar, S.Hymowitz, S.G.Liau, N.Hsu, P.L.McEwan, P.A.Ismaili, M.H.A.Landry, M.L.

(2023) Bioorg Med Chem Lett 89: 129277-129277

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129277
  • Primary Citation of Related Structures:  
    7SZR

  • PubMed Abstract: 

    Inhibition of NF-κB inducing kinase (NIK) has been pursued as a promising therapeutic target for autoimmune disorders due to its highly regulated role in key steps of the NF-κB signaling pathway. Previously reported NIK inhibitors from our group were shown to be potent, selective, and efficacious, but had higher human dose projections than desirable for immunology indications. Herein we report the clearance-driven optimization of a NIK inhibitor guided by metabolite identification studies and structure-based drug design. This led to the identification of an azabicyclo[3.1.0]hexanone motif that attenuated in vitro and in vivo clearance while maintaining NIK potency and increasing selectivity over other kinases, resulting in a greater than ten-fold reduction in predicted human dose.


  • Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States. Electronic address: crawford.james@gene.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 14
A, B
352Mus 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DYQ (Subject of Investigation/LOI)
Query on DYQ

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
1-(3-{[(1R,4R,5S)-4-hydroxy-2-methyl-3-oxo-2-azabicyclo[3.1.0]hexan-4-yl]ethynyl}phenyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide
C21 H17 N5 O3
GMAWUPHGBKLOEK-MRUHUIDDSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.54α = 90
b = 144.54β = 90
c = 46.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-12-20
    Changes: Database references