4Y8C

Crystal structure of phosphodiesterase 9 in complex with (S)-C33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 4Y8C

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 124473.26

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
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
49D
Query on 49D

A, B 6-{[(1S)-1-(4-chlorophenyl)ethyl]amino}-1- cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin- 4-one
C18 H20 Cl N5 O
FIUCLBJMUGCQTF-NSHDSACASA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.205
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 104.72 α = 90.00
b = 104.72 β = 90.00
c = 270.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-02-16
  • Released Date: 2015-09-16
  • Deposition author(s): Huang, M.

Revision History

  • 2015-10-14
    Type: Database references
  • 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations