9LSM | pdb_00009lsm

The crystal structure of PDE5A with L9

• PDB DOI: https://doi.org/10.2210/pdb9LSM/pdb

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


• Deposited: 2025-02-04 Released: 2025-06-18 
• Deposition Author(s): Wu, D., Huang, Y.-Y., Luo, H.-B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.304 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.255 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Plasma metabolites-based drug design: Discovery of novel and highly selective phosphodiesterase 5 inhibitors

Wu, D., Ma, Q., Chen, Y., Yang, G., Zhang, F., Jiang, M., Wang, X., Liu, X., Zhou, Q., Huang, Y.Y., Li, Z., Luo, H.B.

(2025) Chin Chem Lett : 111236

• DOI: https://doi.org/10.1016/j.cclet.2025.111236

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.46 kDa 
• Atom Count: 2,362 
• Modeled Residue Count: 285 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-specific 3',5'-cyclic phosphodiesterase	A	326	Homo sapiens	Mutation(s): 0  Gene Names: PDE5A, PDE5 EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens) Explore O76074  Go to UniProtKB:  O76074
PHAROS:  O76074 GTEx:  ENSG00000138735

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ELC (Subject of Investigation/LOI)	B [auth A]	1-[(13~{S},15~{R})-4-bromanyl-15-(3-chloranyl-4-methoxy-phenyl)-8,12,16-triazatetracyclo[7.7.1.0^{2,7}.0^{13,17}]heptadeca-1(17),2,4,6,8-pentaen-12-yl]ethanone C23 H21 Br Cl N3 O2 DECLLXLSNYPDHY-UXHICEINSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.304 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.255 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.944	α = 90
b = 73.944	β = 90
c = 131.556	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
CrysalisPro	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Wu, D., Huang, Y.-Y., Luo, H.-B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82373732

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release