9LSM | pdb_00009lsm

The crystal structure of PDE5A with L9


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
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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

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesterase326Homo sapiensMutation(s): 0 
Gene Names: PDE5APDE5
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76074
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ELC (Subject of Investigation/LOI)
Query on A1ELC

Download Ideal Coordinates CCD File 
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
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
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 = 73.944α = 90
b = 73.944β = 90
c = 131.556γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
CrysalisProdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82373732

Revision History  (Full details and data files)

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