4GH6

Crystal structure of the PDE9A catalytic domain in complex with inhibitor 28

Structural Biology Knowledgebase: 4GH6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.212

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GH6

Classification: HYDROLASE / Hydrolase Inhibitor

Total Structure Weight: 78528.33

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: UNP residues 241-566
Gene Name(s): PDE9A Gene View

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

A, B N-(4-methoxyphenyl)-N~2~-[1-(2-methylphenyl)- 4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin- 6-yl]-L-alaninamide
C22 H22 N6 O3
VHGPQZWYIWLLDA-AWEZNQCLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LUO N/A in BindingDB
N/A in BindingMoad
IC50: 21 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.212
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.28 α = 90.00
b = 104.28 β = 90.00
c = 270.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-07
  • Released Date: 2012-10-03
  • Deposition author(s): Hou, J., Ke, H.

Revision History

  • 2012-11-14
    Type: Citation | Details: Citation update