4E90

Human phosphodiesterase 9 in complex with inhibitors

Structural Biology Knowledgebase: 4E90 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4E90

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 78696.69

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
Gene Name(s): PDE9A Gene View

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
7RG
Query on 7RG

A, B 6-[(3S,4S)-4-methyl-1-(pyrimidin-2-ylmethyl)pyrrolidin- 3-yl]-1-(tetrahydro-2H-pyran-4-yl)-1,5-dihydro- 4H-pyrazolo[3,4-d]pyrimidin-4-one
C20 H25 N7 O2
IWXUVYOOUMLUTQ-CZUORRHYSA-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 %)
7RG N/A in BindingDB
IC50: 8 nM  BindingMOAD
IC50: 8 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.192
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 103.58 α = 90.00
b = 103.58 β = 90.00
c = 270.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-03-20
  • Released Date: 2013-02-27
  • Deposition author(s): Liu, S.

Revision History

No revisions since initial release