2GTN | pdb_00002gtn

Mutated MAP kinase P38 (Mus Musculus) in complex with Inhbitor PG-951717

• PDB DOI: https://doi.org/10.2210/pdb2GTN/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-04-28 Released: 2006-07-11 
• Deposition Author(s): Walter, R.L., Mekel, M.J., Evdokimov, A.G., Pokross, M.E., Sabat, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.248 (Depositor), 0.340 (DCC) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: other

Literature

The development of novel C-2, C-8, and N-9 trisubstituted purines as inhibitors of TNF-alpha production.

Sabat, M., Vanrens, J.C., Clark, M.P., Brugel, T.A., Maier, J., Bookland, R.G., Laufersweiler, M.J., Laughlin, S.K., Golebiowski, A., De, B., Hsieh, L.C., Walter, R.L., Mekel, M.J., Janusz, M.J.

(2006) Bioorg Med Chem Lett 16: 4360-4365

• PubMed: 16750367 
• DOI: https://doi.org/10.1016/j.bmcl.2006.05.050
• Primary Citation Related Structures: 
  2GTM, 2GTN


• PubMed Abstract: 
  

  A series of C-2, C-8, and N-9 trisubstituted purine based inhibitors of TNF-alpha production are described. The most potent analogs showed low nanomolar activity against LPS-induced TNF-alpha production in a THP-1 cell based assay. The SAR of the series was optimized with the aid of X-ray co-crystal structures of these inhibitors bound with mutated p38 (mp38).

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Organizational Affiliation: 
• Procter and Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, 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: 40.4 kDa 
• Atom Count: 2,972 
• Modeled Residue Count: 337 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	348	Mus musculus	Mutation(s): 0  Gene Names: Mapk14 EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus) Explore P47811  Go to UniProtKB:  P47811

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LIE	C [auth A]	2-(2,6-DIFLUOROPHENOXY)-N-(2-FLUOROPHENYL)-9-ISOPROPYL-9H-PURIN-8-AMINE C20 H16 F3 N5 O OGWSGDLIXOEZJG-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.248 (Depositor), 0.340 (DCC) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.986	α = 90
b = 74.554	β = 90
c = 78.029	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-11 
Deposition Author(s): Walter, R.L., Mekel, M.J., Evdokimov, A.G., Pokross, M.E., Sabat, M.

Revision History  

• Version 1.0: 2006-07-11
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description