3UVP

Human p38 MAP Kinase in Complex with a Benzamide Substituted Benzosuberone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Targeting the Hinge Glycine Flip and the Activation Loop: Novel Approach to Potent p38 alpha Inhibitors.

Martz, K.E., Dorn, A., Baur, B., Schattel, V., Goettert, M.I., Mayer-Wrangowski, S.C., Rauh, D., Laufer, S.A.

(2012) J Med Chem 55: 7862-7874

  • DOI: 10.1021/jm300951u
  • Primary Citation of Related Structures:  
    3UVP

  • PubMed Abstract: 

    • The p38 MAP kinase is a key player in signaling pathways regulating the biosynthesis of inflammatory cytokines. Small molecule p38 inhibitors suppress the production of these cytokines. Therefore p38 is a promising drug target for novel anti-inflamma ...

    The p38 MAP kinase is a key player in signaling pathways regulating the biosynthesis of inflammatory cytokines. Small molecule p38 inhibitors suppress the production of these cytokines. Therefore p38 is a promising drug target for novel anti-inflammatory drugs. In this study, we report novel dibenzepinones, dibenzoxepines, and benzosuberones as p38α MAP kinase inhibitors. Previously reported dibenzepinones and dibenzoxepines were chemically modified by introduction of functional groups or removal of a phenyl ring. This should result in targeting of the hydrophobic region I, the "deep pocket", and the hinge glycine flip of the kinase. Potent inhibitors with IC(50) values in the single digit nanomolar range (up to 3 nM) were identified. Instead of targeting the "deep pocket" in the DFG-out conformation, interactions with the DFG-motif in the in-conformation could be observed by protein X-ray crystallography.

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14A360Homo sapiensMutation(s): 0 
Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A
EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS  Q16539
GTEx  ENSG00000112062
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
048
Query on 048
Download CCD File 
A
N-{2-fluoro-5-[(5-oxo-6,7,8,9-tetrahydro-5H-benzo[7]annulen-2-yl)amino]phenyl}benzamide
C24 H21 F N2 O2
ATBLOTYVKHVLPU-UHFFFAOYSA-N		 Ligand Interaction
BOG
Query on BOG
Download CCD File 
A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
048IC50:  35   nM  BindingDB
048IC50:  35   nM  Binding MOAD
48IC50 :  35   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64α = 90
b = 68.8β = 90
c = 74.8γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-01-16
    Changes: Database references, Structure summary
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary