Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 41.59 kDa 
• Atom Count: 3119 
• Modelled Residue Count: 352 
• Deposited Residue Count: 360 
• Unique protein chains: 1

1WBW

Identification of novel p38 alpha MAP Kinase inhibitors using fragment-based lead generation.

• DOI: 10.2210/pdb1WBW/pdb

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


• Deposited: 2004-11-05 Released: 2005-11-03 
• Deposition Author(s): Tickle, J., Cleasby, A., Devine, L.A., Jhoti, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.273 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

Literature

Identification of Novel P38Alpha Map Kinase Inhibitors Using Fragment-Based Lead Generation

Gill, A., Frederickson, M., Cleasby, A., Woodhead, S.J., Carr, M.G., Woodhead, A.J., Walker, M.T., Congreve, M.S., Devine, L.A., Tisi, D., O'Reilly, M., Seavers, L., Davis, D.J., Curry, J., Anthony, R., Padova, A., Murray, C.W., Carr, R.A.E., Jhoti, H.

(2005) J Med Chem 48: 414

• PubMed: 15658855 
• DOI: 10.1021/jm049575n
• Primary Citation of Related Structures:  
  1W84, 1W83, 1W82, 1WBS, 1WBN, 1WBW, 1WBV, 1WBT


• PubMed Abstract: 
  

We describe the structure-guided optimization of the molecular fragments 2-amino-3-benzyloxypyridine 1 (IC(50) 1.3 mM) and 3-(2-(4-pyridyl)ethyl)indole 2 (IC(50) 35 microM) identified using X-ray crystallographic screening of p38alpha MAP kinase. Using two separate case studies, the article focuses on the key compounds synthesized, the structure-activity relationships and the binding mode observations made during this optimization process, resulting in two potent lead series that demonstrate significant increases in activity. We describe the process of compound elaboration either through the growing out from fragments into adjacent pockets or through the conjoining of overlapping fragments and demonstrate that we have exploited the mobile conserved activation loop, consisting in part of Asp168-Phe169-Gly170 (DFG), to generate significant improvements in potency and kinase selectivity.

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Organizational Affiliation: 

Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom. [e-mail]

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: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.1.37 (PDB Primary Data), 2.7.11.24 (UniProt)
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
NIH Common Fund Data Resources
PHAROS:  Q16539 GTEx:  ENSG00000112062

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LI4	A	3-(1-NAPHTHYLMETHOXY)PYRIDIN-2-AMINE C16 H14 N2 O SZANYTFSQVBOBA-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LI4	IC50:  44000   nM  Binding MOAD
LI4	IC50 :  44000   nM  PDBBind
LI4	IC50:  44000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.273 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.291	α = 90
b = 86.025	β = 90
c = 126.587	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
DENCOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-11-05 
• Released Date: 2005-11-03 
Deposition Author(s): Tickle, J., Cleasby, A., Devine, L.A., Jhoti, H.

Revision History  

• Version 1.0: 2005-11-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance