3T9T | pdb_00003t9t

Crystal structure of BTK mutant (F435T,K596R) complexed with Imidazo[1,5-a]quinoxaline

• PDB DOI: https://doi.org/10.2210/pdb3T9T/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2011-08-03 Released: 2011-10-12 
• Deposition Author(s): Han, S., Caspers, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Imidazo[1,5-a]quinoxalines as irreversible BTK inhibitors for the treatment of rheumatoid arthritis.

Kim, K.H., Maderna, A., Schnute, M.E., Hegen, M., Mohan, S., Miyashiro, J., Lin, L., Li, E., Keegan, S., Lussier, J., Wrocklage, C., Nickerson-Nutter, C.L., Wittwer, A.J., Soutter, H., Caspers, N., Han, S., Kurumbail, R., Dunussi-Joannopoulos, K., Douhan, J., Wissner, A.

(2011) Bioorg Med Chem Lett 21: 6258-6263

• PubMed: 21958547 
• DOI: https://doi.org/10.1016/j.bmcl.2011.09.008
• Primary Citation Related Structures: 
  3T9T


• PubMed Abstract: 
  

  Imidazo[1,5-a]quinoxalines were synthesized that function as irreversible Bruton's tyrosine kinase (BTK) inhibitors. The syntheses and SAR of this series of compounds are presented as well as the X-ray crystal structure of the lead compound 36 in complex with a gate-keeper variant of ITK enzyme. The lead compound showed good in vivo efficacy in preclinical RA models.

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Organizational Affiliation: 
• Medicinal Chemistry, Pfizer, 200 Cambridge Park Drive, Cambridge, MA 02140, United States. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 31.08 kDa 
• Atom Count: 2,303 
• Modeled Residue Count: 263 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ITK/TSK	A	267	Homo sapiens	Mutation(s): 2  Gene Names: ITK, EMT, LYK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q08881 (Homo sapiens) Explore Q08881  Go to UniProtKB:  Q08881
PHAROS:  Q08881 GTEx:  ENSG00000113263

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IAQ	B [auth A]	(2Z)-4-(dimethylamino)-N-{7-fluoro-4-[(2-methylphenyl)amino]imidazo[1,5-a]quinoxalin-8-yl}-N-methylbut-2-enamide C24 H25 F N6 O YMSXHRWUGLAAKL-YFHOEESVSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.34	α = 90
b = 69.35	β = 115.7
c = 47.27	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data collection
PHASER	phasing
REFMAC	refinement
autoPROC	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Han, S., Caspers, N.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2011-10-26
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary