Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 196369.20 
• Atom Count: 11930 
• Residue Count: 1680 
• Unique protein chains: 1

1SO2

CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B In COMPLEX WITH A DIHYDROPYRIDAZINE INHIBITOR

• DOI: 10.2210/pdb1SO2/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2004-03-12 Released: 2004-05-11 
• Deposition Author(s): Scapin, G., Patel, S.B., Chung, C., Varnerin, J.P., Edmondson, S.D., Mastracchio, A., Parmee, E.R., Becker, J.W., Singh, S.B., Van Der Ploeg, L.H., Tota, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.277 
• R-Value Work: 0.232 

Literature

Crystal Structure of Human Phosphodiesterase 3B: Atomic Basis for Substrate and Inhibitor Specificity

Scapin, G., Patel, S.B., Chung, C., Varnerin, J.P., Edmondson, S.D., Mastracchio, A., Parmee, E.R., Singh, S.B., Becker, J.W., Van Der Ploeg, L.H., Tota, M.R.

(2004) Biochemistry 43: 6091-6100

• PubMed: 15147193 
• DOI: 10.1021/bi049868i
• Primary Citation of Related Structures:  
  1SOJ


• PubMed Abstract: 
  

Phosphodiesterases (PDEs) are enzymes that modulate cyclic nucleotide signaling and as such are clinical targets for a range of disorders including congestive heart failure, erectile dysfunction, and inflammation. The PDE3 family comprises two highly homologous subtypes expressed in different tissues, and inhibitors of this family have been shown to increase lipolysis in adipocytes. A specific PDE3B (the lipocyte-localized subtype) inhibitor would be a very useful tool to evaluate the effects of PDE3 inhibition on lipolysis and metabolic rate and might become a novel tool for treatment of obesity. We report here the three-dimensional structures of the catalytic domain of human PDE3B in complex with a generic PDE inhibitor and a novel PDE3 selective inhibitor. These structures explain the dual cAMP/cGMP binding capabilities of PDE3, provide the molecular basis for inhibitor specificity, and can supply a valid platform for the design of improved compounds.

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Organizational Affiliation: 

Departments of Medicinal Chemistry, Merck & Co., Rahway, New Jersey 07065, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
cGMP-inhibited 3',5'-cyclic phosphodiesterase B	A, B, C, D	420	Homo sapiens	Mutation(s): 0  Gene Names: PDE3B EC: 3.1.4.17
Find proteins for Q13370 (Homo sapiens) Go to Gene View: PDE3B Go to UniProtKB:  Q13370

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
666	A, B, C, D	6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE (5R)-6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE C24 H24 I N3 O2 QNURTFDBHAQRSI-OAHLLOKOSA-N
HG9	A, B	1-DEOXY-1-[(2-HYDROXYETHYL)(NONANOYL)AMINO]HEXITOL HG9A-9, NONANOYL-N-HYDROXYETHYLGLUCAMIDE C17 H35 N O7 REPLXGVUTGZQCG-WTTBNOFXSA-N
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
666	IC50: 0.1 - 0.3 nM (100) BINDINGDB
666	IC50: 0.27 nM BINDINGMOAD
666	IC50: 0.27 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.277 
• R-Value Work: 0.232 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 147.482	α = 90.00
b = 121.772	β = 100.74
c = 126.671	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-12 
• Released Date: 2004-05-11 
• Deposition Author(s): Scapin, G., Patel, S.B., Chung, C., Varnerin, J.P., Edmondson, S.D., Mastracchio, A., Parmee, E.R., Becker, J.W., Singh, S.B., Van Der Ploeg, L.H., Tota, M.R.

Revision History 

• Version 1.0: 2004-05-11
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance