1SVH image
Entry Detail
PDB ID:
1SVH
Keywords:
TRANSFERASE
Title:
Crystal Structure of Protein Kinase A in Complex with Azepane Derivative 8
Biological Source:
Source Organism:
Bos taurus,
Host Organism:
Escherichia coli BL21(DE3)
PDB Version:
Deposition Date:
2004-03-29
Release Date:
2005-03-29
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.30 Å
R-Value Free:
0.25
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
1SVH validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:cAMP-dependent protein kinase, alpha-catalytic subunit
Chain IDs:A
Chain Length:350
Number of Molecules:1
Biological Source:Bos taurus
UniProt ID:P00517 Pfam ID:PF00069 EC:2.7.11.11
Protein Blast
Polymer Type:polypeptide(L)
Description:cAMP-dependent protein kinase inhibitor, alpha form
Chain IDs:B
Chain Length:20
Number of Molecules:1
Biological Source:
UniProt ID:P63249 EC:2.7.11.11
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SEP A SER PHOSPHOSERINE
TPO A THR PHOSPHOTHREONINE
Ligand Molecules
I08
Primary Citation
Structure-based optimization of novel azepane derivatives as PKB inhibitors
J.Med.Chem. 47 1375 1390 (2004)
PMID: 14998327 DOI: 10.1021/jm0310479

Abstact

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.

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Primary Citation of related structures
1SVE
1SVG
1VEB