Crystal Structure of NIK with 11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-2-amine (T28)

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Inhibiting NF-KB-inducing kinase (NIK): Discovery, structure-based design, synthesis, structure activity relationship, and co-crystal structures

Li, K.McGee, L.R.Fisher, B.Sudom, A.Liu, J.Rubenstein, S.M.Anwer, M.K.Cushing, T.D.Shin, Y.Ayres, M.Lee, F.Eksterowicz, J.Faulder, P.Waszkowycz, B.Plotnikova, O.Farrelly, E.Xiao, S.H.Chen, G.Wang, Z.

(2013) Bioorg Med Chem Lett 23: 1238-1244

  • DOI: https://doi.org/10.1016/j.bmcl.2013.01.012
  • Primary Citation of Related Structures:  
    4IDT, 4IDV

  • PubMed Abstract: 

    The discovery, structure-based design, synthesis, and optimization of NIK inhibitors are described. Our work began with an HTS hit, imidazopyridinyl pyrimidinamine 1. We utilized homology modeling and conformational analysis to optimize the indole scaffold leading to the discovery of novel and potent conformationally constrained inhibitors such as compounds 25 and 28. Compounds 25 and 31 were co-crystallized with NIK kinase domain to provide structural insights.

  • Organizational Affiliation

    Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA. kli@amgen.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 14
A, B
356Homo sapiensMutation(s): 0 
Gene Names: MAP3K14NIK
UniProt & NIH Common Fund Data Resources
Find proteins for Q99558 (Homo sapiens)
Explore Q99558 
Go to UniProtKB:  Q99558
PHAROS:  Q99558
GTEx:  ENSG00000006062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99558
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on T28

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C15 H13 Br N4
Binding Affinity Annotations 
IDSourceBinding Affinity
T28 Binding MOAD:  4IDT IC50: 100 (nM) from 1 assay(s)
BindingDB:  4IDT IC50: min: 100, max: 4600 (nM) from 2 assay(s)
PDBBind:  4IDT IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.53α = 90
b = 84.53β = 90
c = 117.947γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations