3HP2

Crystal Structure of Human p38alpha complexed with a pyridinone compound

• PDB DOI: https://doi.org/10.2210/pdb3HP2/pdb

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


• Deposited: 2009-06-03 Released: 2009-09-29 
• Deposition Author(s): Shieh, H.-S., Williams, J.M., Stegeman, R.A., Kurumbail, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.252 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Discovery of N-substituted pyridinones as potent and selective inhibitors of p38 kinase.

Selness, S.R., Devraj, R.V., Monahan, J.B., Boehm, T.L., Walker, J.K., Devadas, B., Durley, R.C., Kurumbail, R., Shieh, H., Xing, L., Hepperle, M., Rucker, P.V., Jerome, K.D., Benson, A.G., Marrufo, L.D., Madsen, H.M., Hitchcock, J., Owen, T.J., Christie, L., Promo, M.A., Hickory, B.S., Alvira, E., Naing, W., Blevis-Bal, R.

(2009) Bioorg Med Chem Lett 19: 5851-5856

• PubMed: 19751974 
• DOI: https://doi.org/10.1016/j.bmcl.2009.08.082
• Primary Citation of Related Structures:  
  3HP2, 3HP5


• PubMed Abstract: 
  

  The identification and evolution of a series of potent and selective p38 inhibitors is described. p38 inhibitors based on a N-benzyl pyridinone high-throughput screening hit were prepared and their SAR explored. Their design was guided by ligand bound co-crystals of p38alpha. These efforts resulted in the identification of 12r and 19 as orally active inhibitors of p38 with significant efficacy in both acute and chronic models of inflammation.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Pfizer Corporation, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA. [e-mail]

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: 42.23 kDa 
• Atom Count: 3,022 
• Modelled Residue Count: 341 
• 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: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, MXI2, THP-1 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
P36	B [auth A]	1-benzyl-4-(benzyloxy)-3-bromopyridin-2(1H)-one C19 H16 Br N O2 VBZTXJCTVYBOKW-UHFFFAOYSA-N
I46	C [auth A], D [auth A]	2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine C14 H9 F2 N3 YJCHZVXSPFPKMX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P36	PDBBind:  3HP2	IC50: 680 (nM) from 1 assay(s)
	BindingDB:  3HP2	IC50: 680 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.252 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.246	α = 90
b = 74.44	β = 90
c = 77.238	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Shieh, H.-S., Williams, J.M., Stegeman, R.A., Kurumbail, R.G.

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations