3SHZ

Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3SHZ/pdb

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


• Deposited: 2011-06-17 Released: 2011-08-24 
• Deposition Author(s): Chen, T.T., Chen, T., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.245 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Utilization of Halogen Bond in Lead Optimization: A Case Study of Rational Design of Potent Phosphodiesterase Type 5 (PDE5) Inhibitors.

Xu, Z., Liu, Z., Chen, T., Chen, T.T., Wang, Z., Tian, G., Shi, J., Wang, X., Lu, Y., Yan, X., Wang, G., Jiang, H., Chen, K., Wang, S., Xu, Y., Shen, J., Zhu, W.

(2011) J Med Chem 54: 5607-5611

• PubMed: 21714539 
• DOI: https://doi.org/10.1021/jm200644r
• Primary Citation of Related Structures:  
  3SHY, 3SHZ, 3SIE


• PubMed Abstract: 
  

  For proof-of-concept of halogen bonding in drug design, a series of halogenated compounds were designed based on a lead structure as new inhibitors of phosphodiesterase type 5. Bioassay results revealed a good correlation between the measured bioactivity and the calculated halogen bond energy. Our X-ray crystal structures verified the existence of the predicted halogen bonds, demonstrating that the halogen bond is an applicable tool in drug design and should be routinely considered in lead optimization.

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Organizational Affiliation: 

State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 40.73 kDa 
• Atom Count: 2,350 
• Modelled Residue Count: 297 
• Deposited Residue Count: 347 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-specific 3',5'-cyclic phosphodiesterase	A	347	Homo sapiens	Mutation(s): 0  Gene Names: PDE5, PDE5A 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5CO	B [auth A]	5-chloro-6-ethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one C20 H27 Cl N4 O4 S HVJOKVUJWQTZFF-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5CO	BindingDB:  3SHZ	Kd: 770 (nM) from 1 assay(s)
	PDBBind:  3SHZ	IC50: 35.9 (nM) from 1 assay(s)
	Binding MOAD:  3SHZ	IC50: 35.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.245 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.687	α = 90
b = 74.687	β = 90
c = 131.728	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): Chen, T.T., Chen, T., Xu, Y.C.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations