3JSI

Human phosphodiesterase 9 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 3JSI

Classification: HYDROLASE

Total Structure Weight: 78493.98

Macromolecule Entities
Molecule Chains Length Organism Details
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A A, B 329 Homo sapiens EC#: 3.1.4.35 IUBMB
Fragment: Catalytic domain: UNP residues 242-566
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
WTC
Query on WTC

A, B 6-benzyl-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4- d]pyrimidin-4-one
C17 H18 N4 O
FVOYQCUKGQGDKH-UHFFFAOYSA-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 %)
WTC IC50: 0.8 - 2.1 nM (100) BindingDB

N/A in BindingMoad
IC50: 2.1 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.205
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 104.10 α = 90.00
b = 104.10 β = 90.00
c = 271.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-09-10
  • Released Date: 2009-12-01
  • Deposition author(s): Liu, S.

Revision History

  • 2011-07-13
    Type: Version format compliance