Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 41593.49 
• Atom Count: 2853 
• 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)


• 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 

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:  
  1WBT, 1W84, 1W83, 1W82, 1WBV, 1WBS, 1WBN


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
MITOGEN-ACTIVATED PROTEIN KINASE 14	A	360	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14 (CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A) EC: 2.7.11.24
Find proteins for Q16539 (Homo sapiens) Go to Gene View: MAPK14 Go to UniProtKB:  Q16539

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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 (100) BINDINGDB
LI4	IC50: 44000 nM BINDINGMOAD
LI4	IC50: 44000 nM PDBBIND

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 45.291	α = 90.00
b = 86.025	β = 90.00
c = 126.587	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance