6E9W

Crystal structure of Rock1 with a pyridinylbenzamide based inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Rho-associated protein kinase 1A, B443Homo sapiensMutation(s): 0 
Gene Names: ROCK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13464 (Homo sapiens)
Explore Q13464 
Go to UniProtKB:  Q13464
PHAROS:  Q13464
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13464
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J0P
Query on J0P
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		N-[(2,3-dihydro-1,4-benzodioxin-5-yl)methyl]-4-(pyridin-4-yl)benzamide
C21 H18 N2 O3
FWFHXPGGGOSSPF-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.632α = 90
b = 180.632β = 90
c = 90.294γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction
XDSdata processing

Structure Validation

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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