3JSW

Human PDE9 in complex with selective inhibitor

Structural Biology Knowledgebase: 3JSW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.179

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3JSW

Classification: HYDROLASE

Total Structure Weight: 78608.67

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

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

A, B 6-[(3S,4S)-1-benzyl-4-methylpyrrolidin-3- yl]-1-(1-methylethyl)-1,5-dihydro-4H-pyrazolo[3,4- d]pyrimidin-4-one
C20 H25 N5 O
PUGMRQMXTZPAIZ-RHSMWYFYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
JAR IC50: 66 nM (100) BindingDB

IC50: 66 nM  BindingMOAD
IC50: 66 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.212
  • R-Value Work: 0.179
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 103.28 α = 90.00
b = 103.28 β = 90.00
c = 270.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-09-11
  • Released Date: 2009-12-01
  • Deposition author(s): Liu, S.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4