3QI3

Crystal structure of PDE9A(Q453E) in complex with inhibitor BAY73-6691


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.222

Literature

Macromolecules
Sequence Display for 3QI3

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 124473.02

Macromolecule Entities
Molecule Chains Length Organism Details
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A A, B 533 Homo sapiens EC#: 3.1.4.35 IUBMB
Mutation: Q453E
Gene Name(s): PDE9A Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 1-(2-chlorophenyl)-6-[(2R)-3,3,3-trifluoro- 2-methylpropyl]-1,7-dihydro-4H-pyrazolo[3,4- d]pyrimidin-4-one
C15 H12 Cl F3 N4 O
FFPXPXOAFQCNBS-MRVPVSSYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PDB N/A in BindingDB
N/A in BindingMoad
IC50: 164200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.222
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 103.13 α = 90.00
b = 103.13 β = 90.00
c = 270.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-26
  • Released Date: 2011-04-27
  • Deposition author(s): Hou, J., Xu, J., Liu, M., Zhao, R., Lou, H., Ke, H.

Revision History

  • 2011-07-13
    Type: Version format compliance
  • 2013-11-13
    Type: Non-polymer description
  • 2014-02-19
    Type: Atomic model