ISDA

Entry Detail

PDB ID:

1SVE

Keywords:

TRANSFERASE

Title:

Crystal Structure of Protein Kinase A in Complex with Azepane Derivative 1

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:

2.49 Å

R-Value Free:

0.25

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

P 21 21 21

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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:P61926 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

I01

MG8

Primary Citation

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.Show

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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