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 

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 GTEx:  ENSG00000112062

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)
	Binding MOAD:  4L8M	IC50: 1 (nM) from 1 assay(s)
	PDBBind:  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