4L8M

Human p38 MAP kinase in complex with a Dibenzoxepinone

• PDB DOI:  https://doi.org/10.2210/pdb4L8M/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 2.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

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: https://doi.org/10.1021/jm401276h
• Primary Citation of Related Structures:  
  4L8M


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 42.42 kDa 
• Atom Count: 2,869 
• Modelled Residue Count: 339 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F46	D [auth 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	B [auth A], C [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
F46	BindingDB:  4L8M	Kd: 17 (nM) from 1 assay(s)
		IC50: 1 (nM) from 1 assay(s)
	PDBBind:  4L8M	IC50: 1 (nM) from 1 assay(s)
	Binding MOAD:  4L8M	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.279 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.616	α = 90
b = 72.949	β = 90
c = 76.916	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary