1VEB

Crystal Structure of Protein Kinase A in Complex with Azepane Derivative 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-based optimization of novel azepane derivatives as PKB inhibitors

Breitenlechner, C.B.Wegge, T.Berillon, L.Graul, K.Marzenell, K.Friebe, W.-G.Thomas, U.Schumacher, R.Huber, R.Engh, R.A.Masjost, B.

(2004) J.Med.Chem. 47: 1375-1390

  • DOI: 10.1021/jm0310479
  • Primary Citation of Related Structures:  
  • Also Cited By: 1XHA, 1XH9, 1XH8, 1XH7, 1XH6, 1XH5, 1XH4

  • PubMed Abstract: 
  • Novel azepane derivatives were prepared and evaluated for protein kinase B (PKB-alpha) and protein kinase A (PKA) inhibition. The original (-)-balanol-derived lead structure (4R)-4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzoic acid (3R)-3-[(pyridine ...

    Novel azepane derivatives were prepared and evaluated for protein kinase B (PKB-alpha) and protein kinase A (PKA) inhibition. The original (-)-balanol-derived lead structure (4R)-4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzoic acid (3R)-3-[(pyridine-4-carbonyl)amino]-azepan-4-yl ester (1) (IC(50) (PKB-alpha) = 5 nM) which contains an ester moiety was found to be plasma unstable and therefore unsuitable as a drug. Based upon molecular modeling studies using the crystal structure of the complex between PKA and 1, the five compounds N-[(3R,4R)-4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzoylamino]-azepan-3-yl]-isonicotinamide (4), (3R,4R)-N-[4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzyloxy]-azepan-3-yl]-isonicotinamide (5), N-[(3R,4S)-4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-phenylamino]-methyl]-azepan-3-yl)-isonicotinamide (6), N-[(3R,4R)-4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzylamino]-azepan-3-yl]-isonicotinamide (7), and N-[(3R,4S)-4-(4-[trans-2-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-phenyl]-vinyl]-azepan-3-yl)-isonicotinamide (8) with linkers isosteric to the ester were designed, synthesized, and tested for in vitro inhibitory activity against PKA and PKB-alpha and for plasma stability in mouse plasma.(1) Compound 4 was found to be plasma stable and highly active (IC(50) (PKB-alpha) = 4 nM). Cocrystals with PKA were obtained for 4, 5, and 8 and analyzed for binding interactions and conformational changes in the ligands and protein in order to rationalize the different activities of the molecules.


    Organizational Affiliation

    Pharma Research, Roche Diagnostics GmbH, Werk Penzberg, Nonnenwald 2, D-82372 Penzberg, Germany. birgit.masjost@roche.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase, alpha-catalytic subunit
A
350Bos taurusGene 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
cAMP-dependent protein kinase inhibitor, alpha form
B
20Homo sapiensGene 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
I05
Query on I05

Download SDF File 
Download CCD File 
A
(3R,4R)-N-{4-[4-(2-FLUORO-6-HYDROXY-3-METHOXY-BENZOYL)-BENZYLOXY]-AZEPAN-3-YL}-ISONICOTINAMIDE
C27 H28 F N3 O5
PDMPNESLWSOZQA-IFMALSPDSA-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 %)
I05IC50: 39 nM (100) BINDINGDB
I05IC50: 39 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.881α = 90.00
b = 76.510β = 90.00
c = 80.094γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description