8VXE

Structure of p38 alpha (Mitogen-activated protein kinase 14) complexed with inhibitor 6

• PDB DOI: https://doi.org/10.2210/pdb8VXE/pdb

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


• Deposited: 2024-02-04 Released: 2024-05-08 
• Deposition Author(s): Blaesse, M., Steinbacher, S., Shaffer, P.L., Sharma, S., Thompson, A.A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.289 
• R-Value Work: 0.218 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Structure-Based Optimization of Selective and Brain Penetrant CK1 delta Inhibitors for the Treatment of Circadian Disruptions.

McCarver, S., Hanna, L., Samant, A., Thompson, A.A., Seierstad, M., Saha, A., Wu, D., Lord, B., Sutton, S.W., Shah, V., Milligan, C.M., Wennerholm, M., Shelton, J., Lebold, T.P., Shireman, B.T.

(2024) ACS Med Chem Lett 15: 486-492

• PubMed: 38628796 
• DOI: https://doi.org/10.1021/acsmedchemlett.3c00523
• Primary Citation of Related Structures:  
  8VXD, 8VXE, 8VXF


• PubMed Abstract: 
  

  Neuropsychiatric disorders such as major depressive disorders and schizophrenia are often associated with disruptions to the normal 24 h sleep wake cycle. Casein kinase 1 (CK1δ) is an integral part of the molecular machinery that regulates circadian rhythms. Starting from a cluster of bicyclic pyrazoles identified from a virtual screening effort, we utilized structure-based drug design to identify and reinforce a unique "hinge-flip" binding mode that provides a high degree of selectivity for CK1δ versus the kinome. Pharmacokinetics, brain exposure, and target engagement as measured by ex vivo autoradiography are described for advanced analogs.

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Organizational Affiliation: 

Janssen Research and Development, San Diego, California 92121-1126, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.24 kDa 
• Atom Count: 2,848 
• Modelled Residue Count: 329 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	387	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AD9 (Subject of Investigation/LOI)	B [auth A], C [auth A]	(4M)-4-[3-(4-fluorophenyl)-1-methyl-1H-pyrazol-4-yl]-1H-pyrrolo[2,3-b]pyridine C17 H13 F N4 PURIVPGRKIUWCS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.289 
• R-Value Work: 0.218 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.124	α = 90
b = 74.341	β = 90
c = 78.029	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Blaesse, M., Steinbacher, S., Shaffer, P.L., Sharma, S., Thompson, A.A.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release