4Z3V | pdb_00004z3v

Fragment-Based Discovery of a Small Molecule Reversible Inhibitor of Bruton's Tyrosine Kinase

• PDB DOI: https://doi.org/10.2210/pdb4Z3V/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2015-03-31 Released: 2015-07-01 
• Deposition Author(s): Dougan, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Fragment-Based Discovery of a Small Molecule Inhibitor of Bruton's Tyrosine Kinase.

Smith, C.R., Dougan, D.R., Komandla, M., Kanouni, T., Knight, B., Lawson, J.D., Sabat, M., Taylor, E.R., Vu, P., Wyrick, C.

(2015) J Med Chem 58: 5437-5444

• PubMed: 26087137 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00734
• Primary Citation Related Structures: 
  4Z3V, 4ZLY, 4ZLZ


• PubMed Abstract: 
  

  The discovery and optimization of a series of 4-aminocinnoline-3-carboxamide inhibitors of Bruton's tyrosine kinase are reported. A fragment-based screening approach incorporating X-ray co-crystallography was used to identify a cinnoline fragment and characterize its binding mode in the ATP binding site of Btk. Optimization of the fragment hit resulted in the identification of a lead compound which reduced paw swelling in a dose- and exposure-dependent fashion in a rat model of collagen-induced arthritis.

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Organizational Affiliation: 
• Takeda California, 10410 Science Center Drive, San Diego, California 92121, United States.

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: 33.27 kDa 
• Atom Count: 2,740 
• Modeled Residue Count: 271 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A	283	Homo sapiens	Mutation(s): 0  Gene Names: BTK, AGMX1, ATK, BPK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens) Explore Q06187  Go to UniProtKB:  Q06187
PHAROS:  Q06187 GTEx:  ENSG00000010671

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4L6	F [auth A]	4-amino-8-(5-methyl-1H-indazol-6-yl)cinnoline-3-carboxamide C17 H14 N6 O PTHVKCSYXICMAR-UHFFFAOYSA-N
IMD	B [auth A], C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	D [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.092	α = 90
b = 104.1	β = 90
c = 38.078	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Dougan, D.R.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Database references, Other
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description