3NDM | pdb_00003ndm

Crystal structure of Rho-Associated Protein Kinase (ROCK1) with a potent isoquinolone derivative

• PDB DOI: https://doi.org/10.2210/pdb3NDM/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-06-07 Released: 2010-12-08 
• Deposition Author(s): Li, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.310 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

Substituted 2H-isoquinolin-1-ones as potent Rho-kinase inhibitors: part 3, aryl substituted pyrrolidines.

Bosanac, T., Hickey, E.R., Ginn, J., Kashem, M., Kerr, S., Kugler, S., Li, X., Olague, A., Schlyer, S., Young, E.R.

(2010) Bioorg Med Chem Lett 20: 3746-3749

• PubMed: 20471253 
• DOI: https://doi.org/10.1016/j.bmcl.2010.04.069
• Primary Citation of Related Structures:  
  3NDM


• PubMed Abstract: 
  

  The discovery and SAR of a series of beta-aryl substituted pyrrolidine 2H-isoquinolin-1-one inhibitors of Rho-kinase (ROCK) derived from 2 is herein described. SAR studies have shown that aryl groups in the beta-position are optimal for potency. Our efforts focused on improving the ROCK potency of this isoquinolone class of inhibitors which led to the identification of pyrrolidine 32 which demonstrated a 10-fold improvement in aortic ring (AR) potency over 2.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Boehringer-Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877-0368, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 193.26 kDa 
• Atom Count: 12,746 
• Modelled Residue Count: 1,546 
• Deposited Residue Count: 1,660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho-Associated Protein Kinase (ROCK1)	A, B, C, D	415	Homo sapiens	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13464 (Homo sapiens) Explore Q13464  Go to UniProtKB:  Q13464
PHAROS:  Q13464 GTEx:  ENSG00000067900

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3ND	E [auth B], F [auth C], G [auth D]	(3S,4R)-N-(7-chloro-1-oxo-1,4-dihydroisoquinolin-6-yl)-4-(4-chlorophenyl)pyrrolidine-3-carboxamide C20 H17 Cl2 N3 O2 WWMMSIAGRVSGLG-JKSUJKDBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.310 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.784	α = 90
b = 83.553	β = 119.95
c = 177.962	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
d*TREK	data reduction
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Li, X.

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations