4IDT

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

  • Method: X-RAY DIFFRACTION
  • 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


This is version 1.0 of the entry. See complete history


Literature

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: 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 14A, B356Homo sapiensMutation(s): 0 
Gene Names: MAP3K14NIK
EC: 2.7.11.25
Find proteins for Q99558 (Homo sapiens)
Explore Q99558 
Go to UniProtKB:  Q99558
NIH Common Fund Data Resources
PHAROS:  Q99558
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T28
Query on T28

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-2-amine
C15 H13 Br N4
MEOWHQIIZUZBTO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T28IC50:  100   nM  BindingDB
T28IC50 :  100   nM  PDBBind
T28IC50:  4600   nM  BindingDB
T28IC50:  100   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-17
    Type: Initial release