3QI4

Crystal structure of PDE9A(Q453E) in complex with IBMX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 3QI4

Classification: HYDROLASE

Total Structure Weight: 124204.04

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
IBM
Query on IBM

A, B 3-ISOBUTYL-1-METHYLXANTHINE
C10 H14 N4 O2
APIXJSLKIYYUKG-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 %)
IBM N/A in BindingDB
IC50: 117200 nM  BindingMOAD
IC50: 117200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.213
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 103.41 α = 90.00
b = 103.41 β = 90.00
c = 269.95 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