9YLH | pdb_00009ylh

Human p38 ALPHA MAPK:MW01-8-105SRM N,N-Dimethyl-6-phenyl-5-(4-pyridinyl)-3-pyridazinamine inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb9YLH/pdb

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


• Deposited: 2025-10-08 Released: 2025-11-19 
• Deposition Author(s): Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.239 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Human p38 ALPHA MAPK:MW01-8-105SRM N,N-Dimethyl-6-phenyl-5-(4-pyridinyl)-3-pyridazinamine inhibitor complex

Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.

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: 42.08 kDa 
• Atom Count: 2,868 
• Modeled Residue Count: 339 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CX9	D [auth A]	N,N-dimethyl-6-phenyl-5-(pyridin-4-yl)pyridazin-3-amine C17 H16 N4 JZNLARIEJUCAJO-UHFFFAOYSA-N
GG5	C [auth A]	4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE C14 H10 F N3 BILJSHVAAVZERY-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.239 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.89	α = 90
b = 74.849	β = 90
c = 77.929	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
autoPROC	data reduction
DIMPLE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	AG066722

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release