5K1I | pdb_00005k1i

PDE4 crystal structure in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.258 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5K1I

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Biphenyl Pyridazinone Derivatives as Inhaled PDE4 Inhibitors: Structural Biology and Structure-Activity Relationships.

Gracia, J.Buil, M.A.Castro, J.Eichhorn, P.Ferrer, M.Gavalda, A.Hernandez, B.Segarra, V.Lehner, M.D.Moreno, I.Pages, L.Roberts, R.S.Serrat, J.Sevilla, S.Taltavull, J.Andres, M.Cabedo, J.Vilella, D.Calama, E.Carcasona, C.Miralpeix, M.

(2016) J Med Chem 59: 10479-10497

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00829
  • Primary Citation Related Structures: 
    5K1I

  • PubMed Abstract: 

    Cyclic nucleotide cAMP is a ubiquitous secondary messenger involved in a plethora of cellular responses to biological agents involving activation of adenylyl cyclase. Its intracellular levels are tightly controlled by a family of cyclic nucleotide degrading enzymes, the PDEs. In recent years, cyclic nucleotide phosphodiesterase type 4 (PDE4) has aroused scientific attention as a suitable target for anti-inflammatory therapy in respiratory diseases, particularly in the management of asthma and COPD. Here we describe our efforts to discover novel, highly potent inhaled inhibitors of PDE4. Through structure based design, with the inclusion of a variety of functional groups and physicochemical profiles in order to occupy the solvent-filled pocket of the PDE4 enzyme, we modified the structure of our oral PDE4 inhibitors to reach compounds down to picomolar enzymatic potencies while at the same time tackling successfully an uncovered selectivity issue with the adenosine receptors. In vitro potencies were demonstrated in a rat lung neutrophilia model by administration of a suspension with a Penn-Century MicroSprayer Aerosolizer.


  • Organizational Affiliation
    • Medicinal Chemistry and Screening, ‡Pharmacokinetics and Metabolism, §Experimental Dermatology, and ∥Licensing and Corporate Development, Centro de Investigación y Desarrollo, Almirall S.A. , Crta. Laureà Miró 408-410, Sant Feliu de Llobregat, 08980 Barcelona, Spain.

Macromolecule Content 

  • Total Structure Weight: 304.37 kDa 
  • Atom Count: 21,443 
  • Modeled Residue Count: 2,590 
  • Deposited Residue Count: 2,608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A, B, C, D, E
A, B, C, D, E, F, G, H
326Homo sapiensMutation(s): 0 
Gene Names: PDE4DDPDE3
EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens)
Explore Q08499 
Go to UniProtKB:  Q08499
PHAROS:  Q08499
GTEx:  ENSG00000113448 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08499
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6PT

Query on 6PT



Download:Ideal Coordinates CCD File
AA [auth G]
DA [auth H]
I [auth A]
L [auth B]
O [auth C]
AA [auth G],
DA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
4-[(5-acetyl-2-ethyl-3-oxo-6-phenyl-2,3-dihydropyridazin-4-yl)amino]benzoic acid
C21 H19 N3 O4
HAISKEJFQSPYKC-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
BA [auth G]
EA [auth H]
J [auth A]
M [auth B]
P [auth C]
BA [auth G],
EA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
CA [auth G]
FA [auth H]
K [auth A]
N [auth B]
Q [auth C]
CA [auth G],
FA [auth H],
K [auth A],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6PT BindingDB:  5K1I IC50: 9.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.258 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.444α = 91.01
b = 78.347β = 92.79
c = 161.756γ = 90.08
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description