Dibenzosuberone inhibitor 8e in complex with p38 MAPK

Experimental Data Snapshot

  • Resolution: 2.31 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Design, Synthesis, and Biological Evaluation of Novel Type I(1)/2 p38 alpha MAP Kinase Inhibitors with Excellent Selectivity, High Potency, and Prolonged Target Residence Time by Interfering with the R-Spine.

Walter, N.M.Wentsch, H.K.Buhrmann, M.Bauer, S.M.Doring, E.Mayer-Wrangowski, S.Sievers-Engler, A.Willemsen-Seegers, N.Zaman, G.Buijsman, R.Lammerhofer, M.Rauh, D.Laufer, S.A.

(2017) J Med Chem 60: 8027-8054

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00745
  • Primary Citation of Related Structures:  
    5MTX, 5MTY

  • PubMed Abstract: 

    We recently reported 1a (skepinone-L) as a type I p38α MAP kinase inhibitor with high potency and excellent selectivity in vitro and in vivo. However, as a type I inhibitor, it is entirely ATP-competitive and shows just a moderate residence time. Thus, the scope was to develop a new class of advanced compounds maintaining the structural binding features of skepinone-L scaffold like inducing a glycine flip at the hinge region and occupying both hydrophobic regions I and II. Extending this scaffold with suitable residues resulted in an interference with the kinase's R-Spine. By synthesizing 69 compounds, we could significantly prolong the target residence time with one example to 3663 s, along with an excellent selectivity score of 0.006 and an outstanding potency of 1.0 nM. This new binding mode was validated by cocrystallization, showing all binding interactions typifying type I 1 / 2 binding. Moreover, microsomal studies showed convenient metabolic stability of the most potent, herein reported representatives.

  • Organizational Affiliation

    Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universitaet Tuebingen , Auf der Morgenstelle 8, 72076 Tuebingen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 14360Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens)
Explore Q16539 
Go to UniProtKB:  Q16539
PHAROS:  Q16539
GTEx:  ENSG00000112062 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16539
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HB9

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[2,4-bis(fluoranyl)-5-[[14-(2-hydroxyethylcarbamoyl)-2-oxidanylidene-6-tricyclo[^{3,8}]pentadeca-1(15),3(8),4,6,11,13-hexaenyl]amino]phenyl]thiophene-2-carboxamide
C29 H23 F2 N3 O4 S
Query on BOG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
octyl beta-D-glucopyranoside
C14 H28 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
HB9 BindingDB:  5MTY Kd: min: 1.3, max: 7.5 (nM) from 2 assay(s)
IC50: min: 0.6, max: 35 (nM) from 2 assay(s)
Binding MOAD:  5MTY Kd: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.31 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.118α = 90
b = 70.179β = 90
c = 74.86γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-10-25
    Changes: Database references
  • Version 1.3: 2019-08-14
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Structure summary