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 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaA351Bos taurusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus)
Explore P00517 
Go to UniProtKB:  P00517
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PKI peptideB18Homo sapiensMutation(s): 0 
Gene Names: PKIAPRKACN1
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
PHAROS:  P61925
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J0G (Subject of Investigation/LOI)
Query on J0G

Download Ideal Coordinates CCD File 
C [auth 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
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
J0G Binding MOAD:  6E99 IC50: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.665α = 90
b = 80.632β = 90
c = 103.865γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction

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