4EWQ | pdb_00004ewq

Human p38 alpha MAPK in complex with a pyridazine based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4EWQ/pdb

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


• Deposited: 2012-04-27 Released: 2012-06-27 
• Deposition Author(s): Grum-Tokars, V., Minasov, G., Roy, S., Schavocky, J., Winsor, J., Watterson, D.M., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): Alzheimerss Drug Discovery Foundation (ADDF), National Institutes of Health/National Institute on Aging (NIH/NIA), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

A Selective and Brain Penetrant p38 alpha MAPK Inhibitor Candidate for Neurologic and Neuropsychiatric Disorders That Attenuates Neuroinflammation and Cognitive Dysfunction.

Roy, S.M., Minasov, G., Arancio, O., Chico, L.W., Van Eldik, L.J., Anderson, W.F., Pelletier, J.C., Watterson, D.M.

(2019) J Med Chem 62: 5298-5311

• PubMed: 30978288 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b00058
• Primary Citation Related Structures: 
  4EWQ, 4ZTH


• PubMed Abstract: 
  

  The p38αMAPK is a serine/threonine protein kinase and a key node in the intracellular signaling networks that transduce and amplify stress signals into physiological changes. A preponderance of preclinical data and clinical observations established p38αMAPK as a brain drug discovery target involved in neuroinflammatory responses and synaptic dysfunction in multiple degenerative and neuropsychiatric brain disorders. We summarize the discovery of highly selective, brain-penetrant, small molecule p38αMAPK inhibitors that are efficacious in diverse animal models of neurologic disorders. A crystallography and pharmacoinformatic approach to fragment expansion enabled the discovery of an efficacious hit. The addition of secondary pharmacology screens to refinement delivered lead compounds with improved selectivity, appropriate pharmacodynamics, and efficacy. Safety considerations and additional secondary pharmacology screens drove optimization that delivered the drug candidate MW01-18-150SRM (MW150), currently in early stage clinical trials.

---

Organizational Affiliation: 
• Northwestern University , 320 East Superior Street , Chicago , Illinois 60611 , United States.
Columbia University , New York , New York 10032 , United States.
University of Kentucky , Lexington , Kentucky 40536 , United States.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 45.5 kDa 
• Atom Count: 3,147 
• Modeled Residue Count: 347 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	383	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 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MWL	C [auth A], D [auth A]	3-phenyl-4-(pyridin-4-yl)-6-[4-(pyrimidin-2-yl)piperazin-1-yl]pyridazine C23 H21 N7 OAXXZZBGZDNSGE-UHFFFAOYSA-N
GG5	B [auth A]	4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE C14 H10 F N3 BILJSHVAAVZERY-UHFFFAOYSA-N
PEG	J [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	G [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34ewq

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.257	α = 90
b = 74.276	β = 90
c = 76.815	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
Coot	model building
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Grum-Tokars, V., Minasov, G., Roy, S., Schavocky, J., Winsor, J., Watterson, D.M., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Funding Organization	Location	Grant Number
Alzheimerss Drug Discovery Foundation (ADDF)	United States	261108
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	U01AG043415
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	R01AG031311
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS056051
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS093920

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description