4C1I | pdb_00004c1i

Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System

• PDB DOI: https://doi.org/10.2210/pdb4C1I/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-08-12 Released: 2014-08-27 
• Deposition Author(s): Jorgensen, M., Kehler, J., Langgard, M., Svenstrup, N., Tagmose, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Chapter 4: Selective Inhibitors of Pde2, Pde9, and Pde10: Modulators of Activity of the Central Nervous System

Jorgensen, M., Kehler, J., Langgard, M., Svenstrup, N., Tagmose, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 167.2 kDa 
• Atom Count: 10,670 
• Modelled Residue Count: 1,283 
• Deposited Residue Count: 1,412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CGMP-DEPENDENT 3', 5'-CYCLIC PHOSPHODIESTERASE	A, B, C, D	353	Homo sapiens	Mutation(s): 0  EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for O00408 (Homo sapiens) Explore O00408  Go to UniProtKB:  O00408
PHAROS:  O00408 GTEx:  ENSG00000186642

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EH9	E [auth A], H [auth B], K [auth C], N [auth D]	(2S,3R)-3-(6-amino-9H-purin-9-yl)nonan-2-ol C14 H23 N5 O IOSAAWHGJUZBOG-WDEREUQCSA-N
ZN	F [auth A], I [auth B], L [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	G [auth A], J [auth B], M [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EH9	BindingDB:  4C1I	IC50: min: 635, max: 2620 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.05	α = 110.16
b = 81.81	β = 95.66
c = 93.34	γ = 93.21

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Jorgensen, M., Kehler, J., Langgard, M., Svenstrup, N., Tagmose, L.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary