1SVH | pdb_00001svh

Crystal Structure of Protein Kinase A in Complex with Azepane Derivative 8

PDB DOI: https://doi.org/10.2210/pdb1SVH/pdb

Classification: TRANSFERASE
Organism(s): Bos taurus, Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2004-03-29 Released: 2005-03-29
Deposition Author(s): 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.259 (Depositor)
R-Value Work:
0.212 (Depositor)
R-Value Observed:
0.214 (Depositor)

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

PubMed: 14998327 Search on PubMed
DOI: https://doi.org/10.1021/jm0310479
Primary Citation Related Structures:
1SVE, 1SVG, 1SVH, 1VEB

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-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

Macromolecule Content

Total Structure Weight: 43.42 kDa
Atom Count: 3,048
Modeled Residue Count: 356
Deposited Residue Count: 370
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase, alpha-catalytic subunit	A	350	Bos taurus	Mutation(s): 2 Gene Names: PRKACA EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517 Go to UniProtKB: P00517
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00517
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor, alpha form	B	20	N/A	Mutation(s): 0
UniProt
Find proteins for P63249 (Rattus norvegicus) Explore P63249 Go to UniProtKB: P63249
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63249
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
I08 Query on I08 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3R,4S)-N-(4-{TRANS-2-[4-(2-FLUORO-6-HYDROXY-3-METHOXY-BENZOYL)-PHENYL]-VINYL}-AZEPAN-3-YL)-ISONICOTINAMIDE C₂₈ H₂₈ F N₃ O₄ QXALMENQPNPILV-ANFMQWFKSA-N		Interactions Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.259 (Depositor)
R-Value Work: 0.212 (Depositor)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.166	α = 90
b = 79.155	β = 90
c = 80.587	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-03-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-03-29
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary