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: 41.47 kDa 
• Atom Count: 3171 
• Residue Count: 351 
• Unique protein chains: 1

1WBO

fragment based p38 inhibitors

• DOI: 10.2210/pdb1WBO/pdb

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


• Deposited: 2004-11-04 Released: 2005-01-27 
• Deposition Author(s): Cleasby, A., Devine, L., Gill, A., Jhoti, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.220 
• R-Value Work: 0.167 
• R-Value Observed: 0.167 

Literature

Fragment-Based Lead Discovery Using X-Ray Crystallography

Hartshorn, M.J., Murray, C.W., Cleasby, A., Frederickson, M., Tickle, I.J., Jhoti, H.

(2005) J Med Chem 48: 403

• PubMed: 15658854 
• DOI: 10.1021/jm0495778
• Primary Citation of Related Structures:  
  1W7H, 1WAY, 1WAX, 1WBO, 1WBU, 1WBG, 1WCC


• PubMed Abstract: 
  

Fragment screening offers an alternative to traditional screening for discovering new leads in drug discovery programs. This paper describes a fragment screening methodology based on high throughput X-ray crystallography. The method is illustrated against five proteins (p38 MAP kinase, CDK2, thrombin, ribonuclease A, and PTP1B). The fragments identified have weak potency (>100 microM) but are efficient binders relative to their size and may therefore represent suitable starting points for evolution to good quality lead compounds. The examples illustrate that a range of molecular interactions (i.e., lipophilic, charge-charge, neutral hydrogen bonds) can drive fragment binding and also that fragments can induce protein movement. We believe that the method has great potential for the discovery of novel lead compounds against a range of targets, and the companion paper illustrates how lead compounds have been identified for p38 MAP kinase starting from fragments such as those described in this paper.

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Organizational Affiliation: 

Astex Technology, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom.

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
2CH	A	2-CHLOROPHENOL C6 H5 Cl O ISPYQTSUDJAMAB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
2CH	IC50 :  1000000   nM  PDBBind
2CH	IC50:  1000000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.220 
• R-Value Work: 0.167 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.746	α = 90
b = 84.716	β = 90
c = 126.759	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-11-04 
• Released Date: 2005-01-27 
Deposition Author(s): Cleasby, A., Devine, L., Gill, A., Jhoti, H.

Revision History 

• Version 1.0: 2005-01-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance