6E99

Crystal structure of Protein Kinase A in complex with the PKI peptide and an amino-pyridinylbenzamide based inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.8b01098
  • Primary Citation of Related Structures:  

  • 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 <sub>2 </sub>, 2-F, 3-F) of the pyridine hinge binding motif or replac ...

    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.,AbbVie, Inc. , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States.,AbbVie Deutschland GmbH & Co. KG , Knollstrasse 50 , 67061 , Ludwigshafen , Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
A
351Bos taurusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
Find proteins for P00517 (Bos taurus)
Go to Gene View: PRKACA
Go to UniProtKB:  P00517
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PKI peptide
B
18Homo sapiensMutation(s): 0 
Gene Names: PKIA (PRKACN1)
Find proteins for P61925 (Homo sapiens)
Go to Gene View: PKIA
Go to UniProtKB:  P61925
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J0G
Query on J0G

Download SDF File 
Download CCD File 
A
2-[(2-aminoethyl)amino]-N-[(1R)-1-(3-methoxyphenyl)ethyl]-4-(pyridin-4-yl)benzamide
C23 H26 N4 O2
DVHXGAIYRHHWGU-MRXNPFEDSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
J0GIC50: 1000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.665α = 90.00
b = 80.632β = 90.00
c = 103.865γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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