2H9V

Structural basis for induced-fit binding of Rho-kinase to the inhibitor Y27632


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for induced-fit binding of Rho-kinase to the inhibitor Y-27632

Yamaguchi, H.Miwa, Y.Kasa, M.Kitano, K.Amano, M.Kaibuchi, K.Hakoshima, T.

(2006) J.Biochem.(Tokyo) 140: 305-311

  • DOI: 10.1093/jb/mvj172

  • PubMed Abstract: 
  • Rho-kinase is a main player in the regulation of cytoskeletal events and a promising drug target in the treatment of both vascular and neurological disorders. Here we report the crystal structure of the Rho-kinase catalytic domain in complex with the ...

    Rho-kinase is a main player in the regulation of cytoskeletal events and a promising drug target in the treatment of both vascular and neurological disorders. Here we report the crystal structure of the Rho-kinase catalytic domain in complex with the specific inhibitor Y-27632. Comparison with the structure of PKA bound to this inhibitor revealed a potential induced-fit binding mode that can be accommodated by the phosphate binding loop. This binding mode resembles to that observed in the Rho-kinase-fasudil complex. A structural database search indicated that a pocket underneath the phosphate-binding loop is present that favors binding to a small aromatic ring. Introduction of such a ring group might spawn a new modification scheme of pre-existing protein kinase inhibitors for improved binding capability.


    Organizational Affiliation

    Structural Biology Laboratory, Nara Institute of Science and Technology, and CREST, Japan .




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rho-associated protein kinase 2
A
402Bos taurusMutation(s): 0 
Gene Names: ROCK2
EC: 2.7.11.1
Find proteins for Q28021 (Bos taurus)
Go to Gene View: ROCK2
Go to UniProtKB:  Q28021
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y27
Query on Y27

Download SDF File 
Download CCD File 
A
(R)-TRANS-4-(1-AMINOETHYL)-N-(4-PYRIDYL) CYCLOHEXANECARBOXAMIDE
C14 H21 N3 O
IYOZTVGMEWJPKR-IJLUTSLNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y27Ki: 300 nM (98) BINDINGDB
Y27IC50: 54 - 700 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.232 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 90.781α = 90.00
b = 90.781β = 90.00
c = 341.279γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance