2H9V

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.277 (Depositor) 
  • R-Value Work: 
    0.232 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Y27Click on this verticalbar to view details

This is version 1.3 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 140: 305-311

  • DOI: https://doi.org/10.1093/jb/mvj172
  • Primary Citation of Related Structures:  
    2H9V

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rho-associated protein kinase 2402Bos taurusMutation(s): 0 
EC: 2.7.11.1
UniProt
Find proteins for Q28021 (Bos taurus)
Explore Q28021 
Go to UniProtKB:  Q28021
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ28021
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y27
Query on Y27

Download Ideal Coordinates CCD File 
B [auth A](R)-TRANS-4-(1-AMINOETHYL)-N-(4-PYRIDYL) CYCLOHEXANECARBOXAMIDE
C14 H21 N3 O
IYOZTVGMEWJPKR-IJLUTSLNSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Y27 BindingDB:  2H9V Ki: min: 60, max: 300 (nM) from 4 assay(s)
IC50: min: 8.3, max: 1630 (nM) from 12 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.277 (Depositor) 
  • R-Value Work:  0.232 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.781α = 90
b = 90.781β = 90
c = 341.279γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Y27Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations