6DI5 | pdb_00006di5

CRYSTAL STRUCTURE OF BTK IN COMPLEX WITH COVALENT INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb6DI5/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-22 Released: 2018-09-05 
• Deposition Author(s): Gardberg, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.195 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Discovery of potent, highly selective covalent irreversible BTK inhibitors from a fragment hit.

Qiu, H., Liu-Bujalski, L., Caldwell, R.D., Follis, A.V., Gardberg, A., Goutopoulos, A., Grenningloh, R., Head, J., Johnson, T., Jones, R., Mochalkin, I., Morandi, F., Neagu, C., Sherer, B.

(2018) Bioorg Med Chem Lett 28: 2939-2944

• PubMed: 30122225 
• DOI: https://doi.org/10.1016/j.bmcl.2018.07.008
• Primary Citation Related Structures: 
  6DI3, 6DI5, 6DI9


• PubMed Abstract: 
  

  Bruton's Tyrosine Kinase (BTK) is a member of the TEC kinase family that is expressed in cells of hematopoietic lineage (e.g., in B cells, macrophages, monocytes, and mast cells). Small molecule covalent irreversible BTK inhibitor targeting Cys481 within the ATP-binding pocket, for example ibrutinib, has been applied in the treatment of B-cell malignancies. Starting from a fragment hit, we discovered a novel series of potent covalent irreversible BTK inhibitors that occupy selectivity pocket of the active site of the BTK kinase domain. Guided by X-ray structures and a fragment-based drug design (FBDD) approach, we generated molecules showing comparable cellular potency to ibrutinib and higher kinome selectivity against undesirable off-targets like EGFR.

---

Organizational Affiliation: 
• EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica 01821, MA, USA. Electronic address: [e-mail].
EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica 01821, MA, USA.
Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, USA.
F. Hoffmann-La Roche AG, Konzern-Hauptsitz, Grenzacherstrasse 124, CH-4070 Basel, Switzerland.

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: 32.13 kDa 
• Atom Count: 2,533 
• Modeled Residue Count: 271 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A	271	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GJ7 (Subject of Investigation/LOI)	B [auth A]	2-(4-phenoxyphenoxy)-6-[(1S,4S)-5-propanoyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]pyridine-3-carboxamide C26 H26 N4 O4 DQFJRLJIIQKNPY-ROUUACIJSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.195 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.033	α = 90
b = 107.696	β = 90
c = 39.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Gardberg, A.

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary