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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.287 (Depositor), 0.292 (DCC)
R-Value Work:
0.225 (Depositor), 0.232 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00408
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EH9 Query on EH9 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain O [auth D] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C]	F [auth A], I [auth B], L [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain P [auth D] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C]	G [auth A], J [auth B], M [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
EH9	BindingDB: 4C1I	IC50: 800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.287 (Depositor), 0.292 (DCC)
R-Value Work: 0.225 (Depositor), 0.232 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-08-27

Deposition Author(s):

Revision History (Full details and data files)

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

4C1I | pdb_00004c1i

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

Literature

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

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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