1YQJ

Crystal Structure of p38 Alpha in Complex with a Selective Pyridazine Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1YQJ/pdb

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


• Deposited: 2005-02-01 Released: 2005-04-26 
• Deposition Author(s): Tamayo, N., Liao, H., Goldberg, M., Syed, R., Li, V., Powers, D., Tudor, Y., Yu, V., Wong, M.L., Henkle, B., Middelton, S., Harvey, T., Jang, G., Hungate, R., Dominguez, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.257 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

Design and synthesis of potent pyridazine inhibitors of p38 MAP kinase.

Tamayo, N., Liao, L., Goldberg, M., Powers, D., Tudor, Y.Y., Yu, V., Wong, L.M., Henkle, B., Middleton, S., Syed, R., Harvey, T., Jang, G., Hungate, R., Dominguez, C.

(2005) Bioorg Med Chem Lett 15: 2409-2413

• PubMed: 15837335 
• DOI: https://doi.org/10.1016/j.bmcl.2005.02.010
• Primary Citation of Related Structures:  
  1YQJ


• PubMed Abstract: 
  

  Novel potent trisubstituted pyridazine inhibitors of p38 MAP (mitogen activated protein) kinase are described that have activity in both cell-based assays of cytokine release and animal models of rheumatoid arthritis. They demonstrated potent inhibition of LPS-induced TNF-alpha production in mice and exhibited good efficacy in the rat collagen induced arthritis model.

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Organizational Affiliation: 

Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.55 kDa 
• Atom Count: 3,055 
• Modelled Residue Count: 356 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	366	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, MXI2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
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
6NP	C [auth A]	6((S)-3-BENZYLPIPERAZIN-1-YL)-3-(NAPHTHALEN-2-YL)-4-(PYRIDIN-4-YL)PYRAZINE C30 H27 N5 WFSFNKVFXLIZIY-MHZLTWQESA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
6NP	PDBBind:  1YQJ	Ki: 7.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.257 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.574	α = 90
b = 87.474	β = 90
c = 122.64	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-26 
Deposition Author(s): Tamayo, N., Liao, H., Goldberg, M., Syed, R., Li, V., Powers, D., Tudor, Y., Yu, V., Wong, M.L., Henkle, B., Middelton, S., Harvey, T., Jang, G., Hungate, R., Dominguez, C.

Revision History  

• Version 1.0: 2005-04-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description