1SO2

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.239 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • DOI: 10.1021/bi049868i
  • Primary Citation of Related Structures:  
    1SO2, 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 ...

    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.

    Organizational Affiliation: 

    Departments of Medicinal Chemistry, Merck & Co., Rahway, New Jersey 07065, USA. giovanna_scapin@merck.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cGMP-inhibited 3',5'-cyclic phosphodiesterase BA, B, C, D420Homo sapiensMutation(s): 0 
Gene Names: PDE3B
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q13370 (Homo sapiens)
Explore Q13370 
Go to UniProtKB:  Q13370
PHAROS:  Q13370
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13370
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
666
Query on 666
Download Ideal Coordinates CCD File 
J [auth A],
O [auth B],
R [auth C],
U [auth D]		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		 Ligand Interaction
HG9
Query on HG9
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B],
N [auth B]		1-DEOXY-1-[(2-HYDROXYETHYL)(NONANOYL)AMINO]HEXITOL
C17 H35 N O7
REPLXGVUTGZQCG-WTTBNOFXSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
666 PDBBind:  1SO2 IC50: 0.27 (nM) from 1 assay(s)
BindingDB:  1SO2 IC50: min: 0.11, max: 0.27 (nM) from 2 assay(s)
Binding MOAD:  1SO2 IC50: 0.27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.482α = 90
b = 121.772β = 100.74
c = 126.671γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNXrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

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