Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 30969.51 
• Atom Count: 2136 
• Residue Count: 267 
• Unique protein chains: 1

4C3F

Structure of Lck in complex with a compound discovered by Virtual Fragment Linking

• DOI: 10.2210/pdb4C3F/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 1 


• Deposited: 2013-08-23 Released: 2013-10-23 
• Deposition Author(s): Cowan-Jacob, S.W., Rummel, G., Stark, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.220 
• R-Value Work: 0.177 

Literature

Efficient search of chemical space: navigating from fragments to structurally diverse chemotypes.

Wassermann, A.M., Kutchukian, P.S., Lounkine, E., Luethi, T., Hamon, J., Bocker, M.T., Malik, H.A., Cowan-Jacob, S.W., Glick, M.

(2013) J. Med. Chem. 56: 8879-8891

• PubMed: 24117015 
• DOI: 10.1021/jm401309q


• PubMed Abstract: 
  

We introduce a novel strategy to sample bioactive chemical space, which follows-up on hits from fragment campaigns without the need for a crystal structure. Our results strongly suggest that screening a few hundred or thousand fragments can substantially improve the selection of small-molecule screening subsets. By combining fragment-based screening with virtual fragment linking and HTS fingerprints, we have developed an effective strategy not only to expand from low-affinity hits to potent compounds but also to hop in chemical space to substantially novel chemotypes. In benchmark calculations, our approach accessed subsets of compounds that were substantially enriched in chemically diverse hit compounds for various activity classes. Overall, half of the hits in the screening collection were found by screening only 10% of the library. Furthermore, a prospective application led to the discovery of two structurally novel histone deacetylase 4 inhibitors.

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Organizational Affiliation: 

Novartis Institutes for Biomedical Research Inc. , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TYROSINE-PROTEIN KINASE LCK	A	267	Homo sapiens	Mutation(s): 1  Gene Names: LCK EC: 2.7.10.2
Find proteins for P06239 (Homo sapiens) Go to Gene View: LCK Go to UniProtKB:  P06239

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
7KW	A	N-phenyl-4-(5-phenyl-1H-pyrazol-4-yl)pyrimidin-2-amine C19 H15 N5 GHIDSWLDHRXNQM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.220 
• R-Value Work: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 58.088	α = 90.00
b = 44.596	β = 90.00
c = 120.254	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	phasing
XDS	data reduction
REFMAC	refinement
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-23 
• Released Date: 2013-10-23 
• Deposition Author(s): Cowan-Jacob, S.W., Rummel, G., Stark, W.

Revision History 

• Version 1.0: 2013-10-23
  Type: Initial release
• Version 1.1: 2014-01-15
  Type: Database references
• Version 1.2: 2016-12-14
  Type: Data collection, Other
• Version 1.3: 2018-04-04
  Type: Data collection
• Version 1.4: 2019-02-27
  Type: Data collection, Database references, Experimental preparation