Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 41.90 kDa 
• Atom Count: 2989 
• Modelled Residue Count: 341 
• Deposited Residue Count: 361 
• Unique protein chains: 1

6SFJ

Crystal structure of p38 alpha in complex with compound 77 (MCP41)

• PDB DOI: 10.2210/pdb6SFJ/pdb

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


• Deposited: 2019-08-01 Released: 2019-09-11 
• Deposition Author(s): Chaikuad, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.227 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Fast Iterative Synthetic Approach toward Identification of Novel Highly Selective p38 MAP Kinase Inhibitors.

Rohm, S., Berger, B.T., Schroder, M., Chaikuad, A., Winkel, R., Hekking, K.F.W., Benningshof, J.J.C., Muller, G., Tesch, R., Kudolo, M., Forster, M., Laufer, S., Knapp, S.

(2019) J Med Chem 62: 10757-10782

• PubMed: 31702918 
• DOI: 10.1021/acs.jmedchem.9b01227
• Primary Citation of Related Structures:  
  6SFI, 6SFJ, 6SFK


• PubMed Abstract: 
  

p38 mitogen-activated protein kinases are key mediators of environmental stress response and are promising targets for treatment of inflammatory diseases and cancer. Numerous efforts have led to the discovery of several potent inhibitors; however, so far no highly selective type-II inhibitors have been reported. We previously identified VPC-00628 as a potent and selective type-II inhibitor of p38α/β with few off-targets. Here we analyzed the chemical building blocks of VPC-00628 that played a key role in achieving potency and selectivity through targeting an inactive state of the kinases induced by a unique folded P-loop conformation. Using a rapid, systematic combinatorial synthetic approach, we identified compound 93 ( SR-318 ) with excellent potency and selectivity for p38α/β, which potently inhibited the TNF-α release in whole blood. SR-318 therefore presents a potent and selective type-II inhibitor of p38α/β that can be used as a chemical probe for targeting this particular inactive state of these two p38 isoforms.

---

Organizational Affiliation: 

Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences , Johann Wolfgang Goethe-University , Max-von-Laue-Str. 15 , D-60438 Frankfurt am Main , Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	361	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LBB (Subject of Investigation/LOI)	B [auth A]	~{N}-[5-[[(2~{S})-1-azanyl-4-cyclohexyl-1-oxidanylidene-butan-2-yl]carbamoyl]-2-methyl-phenyl]-1-(2-methylphenyl)pyrazole-4-carboxamide C29 H35 N5 O3 TUROENOKNBFMBG-DEOSSOPVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.227 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.339	α = 90
b = 76.109	β = 90
c = 78.95	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-08-01 
• Released Date: 2019-09-11 
Deposition Author(s): Chaikuad, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2020-01-29
  Changes: Database references