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 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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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 140: 305-311

  • DOI: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Rho-associated protein kinase 2A402Bos taurusMutation(s): 0 
Gene Names: ROCK2
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Y27 BindingDB:  2H9V Ki: min: 60, max: 300 (nM) from 3 assay(s)
IC50: min: 8.3, max: 1630 (nM) from 11 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • 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

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Ligand Structure Quality Assessment 



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