Targeted polypharmacology: crystal structure of the c-Src kinase domain in complex with PP494, a multitargeted kinase inhibitor

Structural Biology Knowledgebase: 3EN5 SBKB.org

Experimental Data Snapshot

  • Resolution: 2.66 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.204

wwPDB Validation Full Report


Sequence Display for 3EN5

Classification: TRANSFERASE

Total Structure Weight: 66104.48

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene tyrosine-protein kinase Src A, B 286 Gallus gallus EC#: IUBMB
Fragment: kinase domain
Gene Name(s): SRC Gene View

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
Query on KS4

A, B 1-cyclobutyl-3-(3,4-dimethoxyphenyl)-1H-pyrazolo[3,4- d]pyrimidin-4-amine
C17 H19 N5 O2
Ligand Explorer
Binding Pocket (JSmol)
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
KS4 IC50: 3000 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Resolution: 2.66 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.204
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.30 α = 101.14
b = 62.99 β = 92.15
c = 74.14 γ = 90.12

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

  • Deposited Date: 2008-09-25
  • Released Date: 2008-10-14
  • Deposition author(s): Blair, J.A., Apsel, B., Knight, Z.A., Shokat, K.M.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4