4IDV

Crystal Structure of NIK with compound 4-{3-[2-amino-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl}-2-methylbut-3-yn-2-ol (13V)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 14A, B, C, D356Homo sapiensMutation(s): 0 
Gene Names: MAP3K14NIK
EC: 2.7.11.25
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13V
Query on 13V

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
4-{3-[2-amino-5-(2-methoxyethoxy)pyrimidin-4-yl]-1H-indol-5-yl}-2-methylbut-3-yn-2-ol
C20 H22 N4 O3
ZZIZLABGKZWVAW-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
13V BindingDB:  4IDV IC50: min: 20, max: 40 (nM) from 2 assay(s)
PDBBind:  4IDV IC50: 40 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.378α = 90
b = 146.014β = 90
c = 254.701γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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