4L6Q

ROCK2 in complex with benzoxaborole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Linking phenotype to kinase: identification of a novel benzoxaborole hinge-binding motif for kinase inhibition and development of high-potency rho kinase inhibitors.

Akama, T.Dong, C.Virtucio, C.Sullivan, D.Zhou, Y.Zhang, Y.K.Rock, F.Freund, Y.Liu, L.Bu, W.Wu, A.Fan, X.Q.Jarnagin, K.

(2013) J.Pharmacol.Exp.Ther. 347: 615-625

  • DOI: 10.1124/jpet.113.207662

  • PubMed Abstract: 
  • Benzoxaboroles are a novel class of drug-like compounds that have been rich sources of novel inhibitors for various enzymes and of new drugs. While examining benzoxaborole activity in phenotypic screens, our attention was attracted by the (aminomethy ...

    Benzoxaboroles are a novel class of drug-like compounds that have been rich sources of novel inhibitors for various enzymes and of new drugs. While examining benzoxaborole activity in phenotypic screens, our attention was attracted by the (aminomethylphenoxy)benzoxaborole family, which potently inhibited Toll-like receptor-stimulated cytokine secretion from leukocytes. After considering their structure-activity relationships and the central role of kinases in leukocyte biology, we performed a kinome-wide screen to investigate the members of the (aminomethylphenoxy)benzoxaborole family. This technique identified Rho-activated kinase (ROCK) as a target. We showed competitive behavior, with respect to ATP, and then determined the ROCK2-drug cocrystal structure. The drug occupies the ATP site in which the oxaborole moiety provides hydrogen bond donors and acceptors to the hinge, and the aminomethyl group interacts with the magnesium/ATP-interacting aspartic acid common to protein kinases. The series exhibits excellent selectivity against most of the kinome, with greater than 15-fold selectivity against the next best member of the AGC protein kinase subfamily. Medicinal chemistry efforts with structure-based design resulted in a compound with a Ki of 170 nM. Cellular studies revealed strong enzyme inhibition rank correlation with suppression of intracellular phosphorylation of a ROCK substrate. The biochemical potencies of these compounds also translated to functional activity, causing smooth muscle relaxation in rat aorta and guinea pig trachea. The series exhibited oral availability and one member reduced rat blood pressure, consistent with ROCK's role in smooth muscle contraction. Thus, the benzoxaborole moiety represents a novel hinge-binding kinase scaffold that may have potential for therapeutic use.


    Organizational Affiliation

    Anacor Pharmaceuticals, Inc., Palo Alto, California.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rho-associated protein kinase 2
A, B
402Homo sapiensMutation(s): 0 
Gene Names: ROCK2 (KIAA0619)
EC: 2.7.11.1
Find proteins for O75116 (Homo sapiens)
Go to Gene View: ROCK2
Go to UniProtKB:  O75116
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1WU
Query on 1WU

Download SDF File 
Download CCD File 
A, B
6-[4-(aminomethyl)-2-fluorophenoxy]-2,1-benzoxaborol-1(3H)-ol
6-[4-(aminomethyl)-2-fluorophenoxy]benzo[c][1,2]oxaborol-1(3H)-ol
C14 H13 B F N O3
TUWUQFIFQVYZSK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.465α = 90.00
b = 147.518β = 125.17
c = 91.214γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
HKL-2000data collection
XDSdata reduction
CCP4model building
Cootmodel building
REFMACrefinement
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-12 
  • Released Date: 2013-10-02 
  • Deposition Author(s): Rock, F., Jarnagin, K.

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-12-18
    Type: Database references
  • Version 1.2: 2018-04-18
    Type: Advisory, Data collection