3HMV

Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification of PDE4B Over 4D subtype-selective inhibitors revealing an unprecedented binding mode

Kranz, M.Wall, M.Evans, B.Miah, A.Ballantine, S.Delves, C.Dombroski, B.Gross, J.Schneck, J.Villa, J.P.Neu, M.Somers, D.O.

(2009) Bioorg Med Chem 17: 5336-5341

  • DOI: 10.1016/j.bmc.2009.03.061
  • Primary Citation of Related Structures:  
    3HMV

  • PubMed Abstract: 
  • A PDE4B over 4D-selective inhibitor programme was initiated to capitalise on the recently discovered predominance of the PDE4B subtype in inflammatory cell regulation. The SAR of a tetrahydrobenzothiophene (THBT) series did not agree with either of two p ...

    A PDE4B over 4D-selective inhibitor programme was initiated to capitalise on the recently discovered predominance of the PDE4B subtype in inflammatory cell regulation. The SAR of a tetrahydrobenzothiophene (THBT) series did not agree with either of two proposed docking modes in the 4B binding site. A subsequent X-ray co-crystal structure determination revealed that the THBT ligand displaces the Gln-443 residue, invariably ligand-anchoring in previous PDE4 co-crystal structures, and even shifts helix-15 by 1-2A. For the first time, several residues of the C-terminus previously proposed to be involved in subtype selectivity are resolved and three of them extend into the ligand binding site potentially allowing for selective drug design.


    Organizational Affiliation

    Medicines Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, England, UK. michael.j.kranz@gsk.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B AB378Homo sapiensMutation(s): 3 
Gene Names: PDE4BDPDE4
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
Find proteins for Q07343 (Homo sapiens)
Explore Q07343 
Go to UniProtKB:  Q07343
NIH Common Fund Data Resources
PHAROS:  Q07343
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HBT
Query on HBT

Download Ideal Coordinates CCD File 
A, B
(6S)-6-methyl-2-{[(2-nitrophenyl)carbonyl]amino}-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide
C17 H17 N3 O4 S
OBHKTNMETRQPKN-VIFPVBQESA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HBTIC50 :  50.119998931884766   nM  PDBBind
HBTIC50:  50   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.309α = 90
b = 57.309β = 90
c = 251.718γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-05-29 
  • Released Date: 2010-06-09 
  • Deposition Author(s): Somers, D.O., Neu, M.

Revision History 

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance