6E9L

Crystal structure of Protein Kinase A in complex with the PKI peptide and a pyridinylbenzamide based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.194 

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: 
  • Co-crystal 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. Aspartic acid residues 176 and 218 in ROCK2, which are glutamic aci ...

    Co-crystal 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. Aspartic acid residues 176 and 218 in ROCK2, which are glutamic acids in PKA, were 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. Substitution (2-Cl, 2-NH2, 2-F, 3-F) of the pyridine hinge binding motif or replacement with pyrimidine afforded compounds with a clean CYP inhibition profile. Finally, compound 16, a potent and selective pan ROCK inhibitor, was shown to be efficacious in the retinal nerve fiber layer model after oral dosing.



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
J0P
Query on J0P

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.085α = 90.00
b = 74.486β = 90.00
c = 79.920γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

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