5T8Q

Crystal structure of murine NF-kappaB inducing kinase (NIK) bound to aryl pyrrole fragment 17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Design of Tricyclic NF-kappa B Inducing Kinase (NIK) Inhibitors That Have High Selectivity over Phosphoinositide-3-kinase (PI3K).

Castanedo, G.M.Blaquiere, N.Beresini, M.Bravo, B.Brightbill, H.Chen, J.Cui, H.F.Eigenbrot, C.Everett, C.Feng, J.Godemann, R.Gogol, E.Hymowitz, S.Johnson, A.Kayagaki, N.Kohli, P.B.Knuppel, K.Kraemer, J.Kruger, S.Loke, P.McEwan, P.Montalbetti, C.Roberts, D.A.Smith, M.Steinbacher, S.Sujatha-Bhaskar, S.Takahashi, R.Wang, X.Wu, L.C.Zhang, Y.Staben, S.T.

(2017) J Med Chem 60: 627-640

  • DOI: 10.1021/acs.jmedchem.6b01363
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We report here structure-guided optimization of a novel series of NF-κB inducing kinase (NIK) inhibitors. Starting from a modestly potent, low molecular weight lead, activity was improved by designing a type 11/2 binding mode that accessed a back poc ...

    We report here structure-guided optimization of a novel series of NF-κB inducing kinase (NIK) inhibitors. Starting from a modestly potent, low molecular weight lead, activity was improved by designing a type 11/2 binding mode that accessed a back pocket past the methionine-471 gatekeeper. Divergent binding modes in NIK and PI3K were exploited to dampen PI3K inhibition while maintaining NIK inhibition within these series. Potent compounds were discovered that selectively inhibit the nuclear translocation of NF-κB2 (p52/REL-B) but not canonical NF-κB1 (REL-A/p50).


    Organizational Affiliation

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



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: Map3k14Nik
EC: 2.7.11.25
Find proteins for Q9WUL6 (Mus musculus)
Go to UniProtKB:  Q9WUL6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
76Y
Query on 76Y

Download CCD File 
A, B
1-[(2-chlorophenyl)methyl]pyrrole-2-carboxamide
C12 H11 Cl N2 O
FNWQVYIDFQBAEE-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.969α = 90
b = 143.969β = 90
c = 46.455γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Database references