2H9V | pdb_00002h9v

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

• PDB DOI: https://doi.org/10.2210/pdb2H9V/pdb

• Classification: TRANSFERASE
• Organism(s): Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2006-06-12 Released: 2006-12-05 
• Deposition Author(s): Yamaguchi, H., Miwa, Y., Kasa, M., Kitano, K., Amano, M., Kaibuchi, K., Hakoshima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.277 (Depositor) 
• R-Value Work: 
  0.232 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

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

• PubMed: 16891330 
• DOI: https://doi.org/10.1093/jb/mvj172
• Primary Citation 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.

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Organizational Affiliation: 
• Structural Biology Laboratory, Nara Institute of Science and Technology, and CREST, Japan .

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 46.02 kDa 
• Atom Count: 3,120 
• Modeled Residue Count: 383 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho-associated protein kinase 2	A	402	Bos taurus	Mutation(s): 0  EC: 2.7.11.1 (PDB Primary Data), 2.7.11.39 (UniProt)
UniProt
Find proteins for Q28021 (Bos taurus) Explore Q28021  Go to UniProtKB:  Q28021

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y27	B [auth A]	(R)-TRANS-4-(1-AMINOETHYL)-N-(4-PYRIDYL) CYCLOHEXANECARBOXAMIDE C14 H21 N3 O IYOZTVGMEWJPKR-IJLUTSLNSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Y27	BindingDB:  2H9V	IC50: 140 (nM) from 1 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), 0.215 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.781	α = 90
b = 90.781	β = 90
c = 341.279	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Yamaguchi, H., Miwa, Y., Kasa, M., Kitano, K., Amano, M., Kaibuchi, K., Hakoshima, T.

Revision History  

• 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