Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42421.40 
• Atom Count: 2826 
• Residue Count: 360 
• Unique protein chains: 1

4L8M

Human p38 MAP kinase in complex with a Dibenzoxepinone

• DOI: 10.2210/pdb4L8M/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2013-06-17 Released: 2013-10-30 
• Deposition Author(s): Richters, A., Mayer-Wrangowski, S.C., Gruetter, C., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.279 
• R-Value Work: 0.221 

Literature

Metabolically Stable Dibenzo[b,e]oxepin-11(6H)-ones as Highly Selective p38 MAP Kinase Inhibitors: Optimizing Anti-Cytokine Activity in Human Whole Blood.

Baur, B., Storch, K., Martz, K.E., Goettert, M.I., Richters, A., Rauh, D., Laufer, S.A.

(2013) J.Med.Chem. 56: 8561-8578

• PubMed: 24131218 
• DOI: 10.1021/jm401276h


• PubMed Abstract: 
  

Five series of metabolically stable disubstituted dibenzo[b,e]oxepin-11(6H)-ones were synthesized and tested in a p38α enzyme assay for their inhibition of tumor necrosis factor-α (TNF-α) release in human whole blood. Compared to the monosubstituted dibenzo[b,e]oxepin-11(6H)-one derivatives, it has been shown that the additional introduction of hydrophilic residues at position 9 leads to a substantial improvement of the inhibitory potency and metabolic stability. Using protein X-ray crystallography, the binding mode of the disubstituted dibenzoxepinones and the induction of a glyince flip in the hinge region were confirmed. The most potent compound of this series, 32e, shows an outstanding biological activity on isolated p38α, with an IC50 value of 1.6 nM, extraordinary selectivity (by a factor >1000, Kinase WholePanelProfiler), and low ATP competitiveness. The ability to inhibit the release of TNF-α from human whole blood was optimized down to an IC50 value of 125 nM. With the promising dibenzoxepinone inhibitor 3i, a pharmacokinetic study in mice was conducted.

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Organizational Affiliation: 

Institute of Pharmacy , Department of Pharmaceutical and Medicinal Chemistry, Eberhard-Karls-University Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A) EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens) Go to Gene View: MAPK14 Go to UniProtKB:  Q16539

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
F46	A	N-[2-fluoro-5-({9-[2-(morpholin-4-yl)ethoxy]-11-oxo-6,11-dihydrodibenzo[b,e]oxepin-3-yl}amino)phenyl]benzamide C33 H30 F N3 O5 OPUXVIDSMSFXIU-UHFFFAOYSA-N
BOG	A	B-OCTYLGLUCOSIDE C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
F46	IC50: 1 nM BINDINGMOAD
F46	IC50: 1 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.279 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 64.616	α = 90.00
b = 72.949	β = 90.00
c = 76.916	γ = 90.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-17 
• Released Date: 2013-10-30 
• Deposition Author(s): Richters, A., Mayer-Wrangowski, S.C., Gruetter, C., Rauh, D.

Revision History 

• Version 1.0: 2013-10-30
  Type: Initial release
• Version 1.1: 2014-02-05
  Type: Database references