3PY1

CDK2 ternary complex with SU9516 and ANS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.199

Literature

Macromolecules
Sequence Display for 3PY1

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 35663.35

Macromolecule Entities
Molecule Chains Length Organism Details
Cell division protein kinase 2 A 306 Homo sapiens EC#: 2.7.11.22 IUBMB
Gene Name(s): CDK2 Gene View CDKN2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 8-ANILINO-1-NAPHTHALENE SULFONATE
C16 H13 N O3 S
FWEOQOXTVHGIFQ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SU9
Query on SU9

A (3Z)-3-(1H-IMIDAZOL-5-YLMETHYLENE)-5-METHOXY- 1H-INDOL-2(3H)-ONE
SU9516 (Synonym)
C13 H11 N3 O2
QNUKRWAIZMBVCU-WCIBSUBMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
2AN N/A in BindingDB
Kd: 37000 nM  BindingMOAD

SU9 IC50: 22 - 35 nM (100) BindingDB

IC50: 130 nM  BindingMOAD
IC50: 130 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.199
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 53.35 α = 90.00
b = 70.19 β = 90.00
c = 71.48 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-12-10
  • Released Date: 2011-02-16
  • Deposition author(s): Betzi, S., Alam, R., Schonbrunn, E.

Revision History

  • Version 1_0: 2011-02-16

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance