3WBL

Crystal structure of CDK2 in complex with pyrazolopyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 3WBL

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 34401.99

Macromolecule Entities
Molecule Chains Length Organism Details
Cyclin-dependent kinase 2 A 298 Homo sapiens EC#: 2.7.11.22 IUBMB
Gene Name(s): CDK2 Gene View CDKN2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A N~7~-(4-ethoxyphenyl)-6-methyl-N~5~-[(3S)- piperidin-3-yl]pyrazolo[1,5-a]pyrimidine- 5,7-diamine
5- a]pyrimidin-7-yl)}(4-ethoxyphenyl)amine, (Synonym)
C20 H26 N6 O
WJOUGMPFYANZMI-INIZCTEOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PDY IC50: 23000 nM (100) BindingDB

IC50: 23000 nM  BindingMOAD
IC50: 23000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.189
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 53.65 α = 90.00
b = 72.10 β = 90.00
c = 72.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-20
  • Released Date: 2013-10-30
  • Deposition author(s): Fujino, A., Fukushima, K., Kubota, T., Kosugi, T., Takimoto-Kamimura, M.

Revision History

  • Version 1_0: 2013-10-30

    Type: Initial release