1UDU

Crystal structure of Human Phosphodiesterase 5 complexed with tadalafil(Cialis)

• PDB DOI:  https://doi.org/10.2210/pdb1UDU/pdb

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


• Deposited: 2003-05-06 Released: 2004-05-11 
• Deposition Author(s): Sung, B.-J., Lee, J.I., Heo, Y.-S., Kim, J.H., Moon, J., Yoon, J.M., Hyun, Y.-L., Kim, E., Eum, S.J., Lee, T.G., Cho, J.M., Park, S.-Y., Lee, J.-O., Jeon, Y.H., Hwang, K.Y., Ro, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.374 
• R-Value Work: 0.263 
• R-Value Observed: 0.263 

Literature

Structure of the catalytic domain of human phosphodiesterase 5 with bound drug molecules

Sung, B.-J., Hwang, K.Y., Jeon, Y.H., Lee, J.I., Heo, Y.-S., Kim, J.H., Moon, J., Yoon, J.M., Hyun, Y.-L., Kim, E., Eum, S.J., Park, S.-Y., Lee, J.-O., Lee, T.G., Ro, S., Cho, J.M.

(2003) Nature 425: 98-102

• PubMed: 12955149 
• DOI: https://doi.org/10.1038/nature01914
• Primary Citation of Related Structures:  
  1UDT, 1UDU, 1UHO


• PubMed Abstract: 
  

Phosphodiesterases (PDEs) are a superfamily of enzymes that degrade the intracellular second messengers cyclic AMP and cyclic GMP. As essential regulators of cyclic nucleotide signalling with diverse physiological functions, PDEs are drug targets for the treatment of various diseases, including heart failure, depression, asthma, inflammation and erectile dysfunction. Of the 12 PDE gene families, cGMP-specific PDE5 carries out the principal cGMP-hydrolysing activity in human corpus cavernosum tissue. It is well known as the target of sildenafil citrate (Viagra) and other similar drugs for the treatment of erectile dysfunction. Despite the pressing need to develop selective PDE inhibitors as therapeutic drugs, only the cAMP-specific PDE4 structures are currently available. Here we present the three-dimensional structures of the catalytic domain (residues 537-860) of human PDE5 complexed with the three drug molecules sildenafil, tadalafil (Cialis) and vardenafil (Levitra). These structures will provide opportunities to design potent and selective PDE inhibitors with improved pharmacological profiles.

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Organizational Affiliation: 

Division of Drug Discovery, CrystalGenomics, Inc., Daedeok Biocommunity, Jeonmin-dong, Yuseong-gu, Daejeon, 305-390, South Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.02 kDa 
• Atom Count: 5,146 
• Modelled Residue Count: 626 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-specific 3',5'-cyclic phosphodiesterase	A, B	324	Homo sapiens	Mutation(s): 0  Gene Names: PDE5A, PDE5 EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens) Explore O76074  Go to UniProtKB:  O76074
PHAROS:  O76074

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIA	E [auth A], H [auth B]	6-BENZO[1,3]DIOXOL-5-YL-2-METHYL-2,3,6,7,12,12A-HEXAHYDRO-PYRAZINO[1',2':1,6]PYRIDO[3,4-B]INDOLE-1,4-DIONE C22 H19 N3 O4 WOXKDUGGOYFFRN-IIBYNOLFSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CIA	BindingDB:  1UDU	Ki: min: 5, max: 10 (nM) from 3 assay(s)
		IC50: min: 1.2, max: 12 (nM) from 13 assay(s)
		EC50: 78 (nM) from 1 assay(s)
	PDBBind:  1UDU	Kd: 0.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.374 
• R-Value Work: 0.263 
• R-Value Observed: 0.263 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.352	α = 90
b = 48.561	β = 117.28
c = 123.863	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-11 
Deposition Author(s): Sung, B.-J., Lee, J.I., Heo, Y.-S., Kim, J.H., Moon, J., Yoon, J.M., Hyun, Y.-L., Kim, E., Eum, S.J., Lee, T.G., Cho, J.M., Park, S.-Y., Lee, J.-O., Jeon, Y.H., Hwang, K.Y., Ro, S.

Revision History  

• Version 1.0: 2004-05-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance