3K3H

Crystal structure of the PDE9A catalytic domain in complex with (S)-BAY73-6691


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.223

Literature

Macromolecules
Sequence Display for 3K3H

Classification: HYDROLASE

Total Structure Weight: 77986.03

Macromolecule Entities
Molecule Chains Length Organism Details
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A A, B 326 Homo sapiens EC#: 3.1.4.35 IUBMB
Fragment: Catalytic domain: UNP residues 241-566
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
BYE
Query on BYE

A, B 1-(2-chlorophenyl)-6-[(2S)-3,3,3-trifluoro- 2-methylpropyl]-1,7-dihydro-4H-pyrazolo[3,4- d]pyrimidin-4-one
C15 H12 Cl F3 N4 O
FFPXPXOAFQCNBS-QMMMGPOBSA-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 %)
BYE N/A in BindingDB
N/A in BindingMoad
IC50: 88 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.223
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 103.27 α = 90.00
b = 103.27 β = 90.00
c = 271.10 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-02
  • Released Date: 2010-02-16
  • Deposition author(s): Wang, H., Luo, X., Ye, M., Hou, J., Robinson, H., Ke, H.

Revision History

  • Version 1_0: 2010-02-16

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance

  • Version 1_2: 2013-11-13

    Type: Non-polymer description