1WBN

fragment based p38 inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb1WBN/pdb

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


• Deposited: 2004-11-04 Released: 2005-11-03 
• Deposition Author(s): Cleasby, A., Devine, L.A., Gill, A.L., Jhoti, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.244 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Literature

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

Gill, A.L., 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.C., Davis, D.J., Curry, J., Anthony, R., Padova, A., Murray, C.W., Carr, R.A., Jhoti, H.

(2005) J Med Chem 48: 414

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


• 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]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 41.74 kDa 
• Atom Count: 3,414 
• Modelled Residue Count: 352 
• Deposited Residue Count: 360 
• Unique protein chains: 1

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)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L09	B [auth A]	N-(3-TERT-BUTYL-1H-PYRAZOL-5-YL)-N'-{4-CHLORO-3-[(PYRIDIN-3-YLOXY)METHYL]PHENYL}UREA C20 H22 Cl N5 O2 NTMADESEDXKNFZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
L09	Binding MOAD:  1WBN	IC50: 350 (nM) from 1 assay(s)
	PDBBind:  1WBN	IC50: 350 (nM) from 1 assay(s)
	BindingDB:  1WBN	IC50: 350 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.244 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.141	α = 90
b = 86.001	β = 90
c = 125.729	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-03 
Deposition Author(s): Cleasby, A., Devine, L.A., Gill, A.L., 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