2I0H

The structure of p38alpha in complex with an arylpyridazinone

• PDB DOI: https://doi.org/10.2210/pdb2I0H/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-08-10 Released: 2006-10-17 
• Deposition Author(s): Natarajan, S.R., Heller, S.T., Nam, K., Singh, S.B., Scapin, G., Patel, S., Thompson, J.E., Fitzgerald, C.E., O'Keefe, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

p38 MAP Kinase Inhibitors Part 6: 2-Arylpyridazin-3-ones as templates for inhibitor design.

Natarajan, S.R., Heller, S.T., Nam, K., Singh, S.B., Scapin, G., Patel, S., Fitzgerald, C.E., Thompson, J.E., O'Keefe, S.J.

(2006) Bioorg Med Chem Lett 16: 5809-5813

• PubMed: 16945533 
• DOI: https://doi.org/10.1016/j.bmcl.2006.08.074
• Primary Citation of Related Structures:  
  2I0H


• PubMed Abstract: 
  

  p38 inhibitors based on 3,4-dihydropyrido[4,3-d]pyrimidazin-2-one template were synthesized and their SAR explored. Benchmark compounds 30, 35, and 36 were found to be potent against the enzyme. Crystal structure of p38 in complex with 30 indicated a key pi-stacking interaction with the pendant tyrosine residue-35 in the glycine-rich loop.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, 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: 43.24 kDa 
• Atom Count: 3,384 
• Modelled Residue Count: 349 
• 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): 1  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, MXI2 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
222	B [auth A], C [auth A]	2-(3-{(2-CHLORO-4-FLUOROPHENYL)[1-(2-CHLOROPHENYL)-6-OXO-1,6-DIHYDROPYRIDAZIN-3-YL]AMINO}PROPYL)-1H-ISOINDOLE-1,3(2H)-DIONE C27 H19 Cl2 F N4 O3 QGJNGXXVCVFADC-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
222	PDBBind:  2I0H	IC50: 9 (nM) from 1 assay(s)
	BindingDB:  2I0H	IC50: 9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.722	α = 90
b = 88.225	β = 90
c = 121.456	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-17 
Deposition Author(s): Natarajan, S.R., Heller, S.T., Nam, K., Singh, S.B., Scapin, G., Patel, S., Thompson, J.E., Fitzgerald, C.E., O'Keefe, S.J.

Revision History  

• Version 1.0: 2006-10-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description