6ED6

Crystal structure of Rock2 with a pyridinylbenzamide based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of Selective Dual ROCK1 and ROCK2 Inhibitors Using Structure Based Drug Design.

Hobson, A.D.Judge, R.A.Aguirre, A.L.Brown, B.S.Cui, Y.Ding, P.Dominguez, E.DiGiammarino, E.Egan, D.A.Freiberg, G.M.Gopalakrishnan, S.M.Harris, C.M.Honore, M.P.Kage, K.L.Kapecki, N.J.Ling, C.Ma, J.Mack, H.Mamo, M.Maurus, S.McRae, B.Moore, N.S.Mueller, B.K.Mueller, R.Namovic, M.T.Patel, K.Pratt, S.D.Putman, C.B.Queeney, K.L.Sarris, K.K.Schaffter, L.M.Stoll, V.S.Vasudevan, A.Wang, L.Wang, L.Wirthl, W.Yach, K.

(2018) J Med Chem 61: 11074-11100

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01098
  • Primary Citation of Related Structures:  
    6E99, 6E9L, 6E9W, 6ED6

  • PubMed Abstract: 

    A HTS campaign identified compound 1, an excellent hit-like molecule to initiate medicinal chemistry efforts to optimize a dual ROCK1 and ROCK2 inhibitor. Substitution (2-Cl, 2-NH 2 , 2-F, 3-F) of the pyridine hinge binding motif or replacement with pyrimidine afforded compounds with a clean CYP inhibition profile. Cocrystal structures of an early lead compound were obtained in PKA, ROCK1, and ROCK2. This provided critical structural information for medicinal chemistry to drive compound design. The structural data indicated the preferred configuration at the central benzylic carbon would be ( R), and application of this information to compound design resulted in compound 16. This compound was shown to be a potent and selective dual ROCK inhibitor in both enzyme and cell assays and efficacious in the retinal nerve fiber layer model after oral dosing. This tool compound has been made available through the AbbVie Compound Toolbox. Finally, the cocrystal structures also identified that aspartic acid residues 176 and 218 in ROCK2, which are glutamic acids in PKA, could be targeted as residues to drive both potency and kinome selectivity. Introduction of a piperidin-3-ylmethanamine group to the compound series resulted in compound 58, a potent and selective dual ROCK inhibitor with excellent predicted drug-like properties.


  • Organizational Affiliation

    AbbVie Bioresearch Center , 381 Plantation Street , Worcester , Massachusetts 01605 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rho-associated protein kinase 2
A, B
415Homo sapiensMutation(s): 0 
Gene Names: ROCK2KIAA0619
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75116 (Homo sapiens)
Explore O75116 
Go to UniProtKB:  O75116
PHAROS:  O75116
GTEx:  ENSG00000134318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75116
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J0P (Subject of Investigation/LOI)
Query on J0P

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-[(2,3-dihydro-1,4-benzodioxin-5-yl)methyl]-4-(pyridin-4-yl)benzamide
C21 H18 N2 O3
FWFHXPGGGOSSPF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.446α = 90
b = 136.672β = 90
c = 148.691γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references