3EL8

Crystal structure of c-Src in complex with pyrazolopyrimidine 5

Structural Biology Knowledgebase: 3EL8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 3EL8

Classification: TRANSFERASE

Total Structure Weight: 65909.19

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene tyrosine-protein kinase Src A, B 286 Gallus gallus EC#: 2.7.10.2 IUBMB
Fragment: Protein kinase domain: UNP residues 251-533
Gene Name(s): SRC Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PD5
Query on PD5

A 1-{4-[4-amino-1-(1-methylethyl)-1H-pyrazolo[3,4- d]pyrimidin-3-yl]phenyl}-3-[3-(trifluoromethyl)phenyl]urea
1-(4-(4-amino-1-isopropyl-1H-pyrazolo[3,4- d]pyrimidin-3-yl)phenyl)-3-(3-(trifluoromethyl)phenyl)urea (Synonym)
C22 H20 F3 N7 O
LEERPLGXOHLQPF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PD5 N/A in BindingDB
IC50: 25 nM  BindingMOAD
IC50: 25 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.218
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 42.38 α = 101.01
b = 63.69 β = 90.25
c = 73.79 γ = 90.12

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-20
  • Released Date: 2008-10-28
  • Deposition author(s): Dar, A.C., Lopez, M.S., Shokat, K.M.

Revision History

  • 2011-12-07
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4