9LRN | pdb_00009lrn

The crystal structure of PDE2A with 13t

PDB DOI: https://doi.org/10.2210/pdb9LRN/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2025-01-31 Released: 2026-05-27
Deposition Author(s): Huang, Y.-Y., Luo, H.-B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.300 (Depositor), 0.303 (DCC)
R-Value Work:
0.244 (Depositor), 0.248 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery of A phosphodiesterase 2 Inhibitor Containing 6-fluoroquinoline-8-carboxamide Moiety for the Treatment of Alzheimer's disease

Xu, C., Huang, Y.-Y., Luo, H.-B.

To be published.

Macromolecule Content

Total Structure Weight: 425.28 kDa
Atom Count: 10,142
Modeled Residue Count: 1,239
Deposited Residue Count: 3,764
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	941	Homo sapiens	Mutation(s): 0 Gene Names: PDE2A 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
A1EK7 (Subject of Investigation/LOI) Query on A1EK7 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], P [auth D]	6-fluoranyl-~{N}-[(1~{S})-2-oxidanyl-1-[4-(trifluoromethyloxy)phenyl]ethyl]quinoline-8-carboxamide C₁₉ H₁₄ F₄ N₂ O₃ HEEXCMZRIVVGEB-MRXNPFEDSA-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]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-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]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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]