8YD9 | pdb_00008yd9

Crystal structure of p38alpha with an allosteric inhibitor 3

• PDB DOI: https://doi.org/10.2210/pdb8YD9/pdb

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


• Deposited: 2024-02-19 Released: 2025-02-26 
• Deposition Author(s): Hasegawa, S., Kinoshita, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.205 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Identification of a novel target site for ATP-independent p38 alpha inhibitors

Kinoshita, T., Hasegawa, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.29 kDa 
• Atom Count: 3,488 
• Modeled Residue Count: 350 
• 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
6GI (Subject of Investigation/LOI)	B [auth A]	13-[4-({Imidazo[1,2-a]pyridin-2-yl}methoxy)phenyl]-4,8-dioxa-12,14,16,18-tetraazatetracyclo[9.7.0.0^{3,9}.0^{12,17}]octadeca-1(11),2,9,15,17-pentaen-15-amine C26 H23 N7 O3 YNNIPDFDZWDMRE-XMMPIXPASA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.205 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.785	α = 90
b = 85.643	β = 90
c = 126.935	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Hasegawa, S., Kinoshita, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release