4OTF

Crystal structure of the kinase domain of Bruton's Tyrosine kinase with GDC0834

• PDB DOI:  https://doi.org/10.2210/pdb4OTF/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-02-13 Released: 2015-01-28 
• Deposition Author(s): Hymowitz, S.G., Maurer, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

wwPDB Validation 

Currently 4OTF does not have a validation slider image.

Literature

Potent and selective Bruton's tyrosine kinase inhibitors: Discovery of GDC-0834.

Young, W.B., Barbosa, J., Blomgren, P., Bremer, M.C., Crawford, J.J., Dambach, D., Gallion, S., Hymowitz, S.G., Kropf, J.E., Lee, S.H., Liu, L., Lubach, J.W., Macaluso, J., Maciejewski, P., Maurer, B., Mitchell, S.A., Ortwine, D.F., Di Paolo, J., Reif, K., Scheerens, H., Schmitt, A., Sowell, C.G., Wang, X., Wong, H., Xiong, J.M., Xu, J., Zhao, Z., Currie, K.S.

(2015) Bioorg Med Chem Lett 25: 1333-1337

• PubMed: 25701252 
• DOI: https://doi.org/10.1016/j.bmcl.2015.01.032
• Primary Citation of Related Structures:  
  4OTF


• PubMed Abstract: 
  

SAR studies focused on improving the pharmacokinetic (PK) properties of the previously reported potent and selective Btk inhibitor CGI-1746 (1) resulted in the clinical candidate GDC-0834 (2), which retained the potency and selectivity of CGI-1746, but with much improved PK in preclinical animal models. Structure based design efforts drove this work as modifications to 1 were investigated at both the solvent exposed region as well as 'H3 binding pocket'. However, in vitro metabolic evaluation of 2 revealed a non CYP-mediated metabolic process that was more prevalent in human than preclinical species (mouse, rat, dog, cyno), leading to a high-level of uncertainly in predicting human pharmacokinetics. Due to its promising potency, selectivity, and preclinical efficacy, a single dose IND was filed and 2 was taken in to a single dose phase I trial in healthy volunteers to quickly evaluate the human pharmacokinetics. In human, 2 was found to be highly labile at the exo-cyclic amide bond that links the tetrahydrobenzothiophene moiety to the central aniline ring, resulting in insufficient parent drug exposure. This information informed the back-up program and discovery of improved inhibitors.

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Organizational Affiliation: 

Gilead Sciences, 36 East Industrial Rd., Branford, CT 06405, United States (formerly CGI Pharmaceuticals).

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: 32.62 kDa 
• Atom Count: 2,413 
• Modelled Residue Count: 263 
• 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: AGMX1, ATK, BPK, BTK 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2VL	E [auth A]	N-{3-[6-({4-[(2R)-1,4-dimethyl-3-oxopiperazin-2-yl]phenyl}amino)-4-methyl-5-oxo-4,5-dihydropyrazin-2-yl]-2-methylphenyl }-4,5,6,7-tetrahydro-1-benzothiophene-2-carboxamide C33 H36 N6 O3 S CDOOFZZILLRUQH-GDLZYMKVSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	A	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
2VL	BindingDB:  4OTF	IC50: min: 2.3, max: 60 (nM) from 4 assay(s)
		EC50: min: 350, max: 380 (nM) from 2 assay(s)
	Binding MOAD:  4OTF	IC50: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.203 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.507	α = 90
b = 108.507	β = 90
c = 42.221	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Currently 4OTF does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Hymowitz, S.G., Maurer, B.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary