4OEW | pdb_00004oew

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

• PDB DOI: https://doi.org/10.2210/pdb4OEW/pdb
• Entry: 4OEW supersedes: 3TSF

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-14 Released: 2015-04-01 
• Deposition Author(s): Chen, T.T., Ren, J., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 
  0.259 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Thermodynamic and structural characterization of halogen bonding in protein-ligand interactions: a case study of PDE5 and its inhibitors.

Ren, J., He, Y., Chen, W., Chen, T., Wang, G., Wang, Z., Xu, Z., Luo, X., Zhu, W., Jiang, H., Shen, J., Xu, Y.

(2014) J Med Chem 57: 3588-3593

• PubMed: 24702184 
• DOI: https://doi.org/10.1021/jm5002315
• Primary Citation Related Structures: 
  4OEW, 4OEX


• PubMed Abstract: 
  

  The significance of halogen bonding in protein-ligand interactions has been recognized recently. We present here the first comprehensive thermodynamic and structural characterization of halogen bonding in PDE5-inhibitor interactions. ITC studies reveal that binding strength of the halogen bonding between chlorine, bromine, and iodine of inhibitor and the protein is -1.57, -3.09, and -5.59 kJ/mol, respectively. The halogens interact with the designed residue Y612 and an unexpected buried water molecule.

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Organizational Affiliation: 
• CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS) , 555 Zuchongzhi Road, Shanghai 201203, 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: 2,390 
• Modeled Residue Count: 289 
• 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
5IO	D [auth A]	6-ethyl-5-iodo-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one C20 H27 I N4 O4 S CLYYLXSJJMHCHN-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5IO	BindingDB:  4OEW	Kd: 150 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free:  0.259 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.12	α = 90
b = 74.12	β = 90
c = 131.8	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Chen, T.T., Ren, J., Xu, Y.C.
• This entry supersedes: 3TSF

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations