4IDT | pdb_00004idt

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

• PDB DOI: https://doi.org/10.2210/pdb4IDT/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2012-12-13 Released: 2013-04-17 
• Deposition Author(s): Liu, J., Sudom, A., Wang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.228 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

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

• PubMed: 23374866 
• DOI: https://doi.org/10.1016/j.bmcl.2013.01.012
• Primary Citation 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.

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Organizational Affiliation: 
• Amgen Inc., 1120 Veterans Boulevard, South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.01 kDa 
• Atom Count: 5,562 
• Modeled Residue Count: 669 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 14	A, B	356	Homo sapiens	Mutation(s): 0  Gene Names: MAP3K14, NIK 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T28	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.228 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.53	α = 90
b = 84.53	β = 90
c = 117.947	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Liu, J., Sudom, A., Wang, Z.

Revision History  

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