6KK0

Crystal structure of PDE4D catalytic domain complexed with compound 4e


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery and Optimization of alpha-Mangostin Derivatives as Novel PDE4 Inhibitors for the Treatment of Vascular Dementia.

Liang, J.Huang, Y.Y.Zhou, Q.Gao, Y.Li, Z.Wu, D.Yu, S.Guo, L.Chen, Z.Huang, L.Liang, S.H.He, X.Wu, R.Luo, H.B.

(2020) J Med Chem 63: 3370-3380

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00060
  • Primary Citation of Related Structures:  
    6KJZ, 6KK0

  • PubMed Abstract: 

    To validate PDE4 inhibitors as novel therapeutic agents against vascular dementia (VaD), 25 derivatives were discovered from the natural inhibitor α-mangostin (IC 50 = 1.31 μM). Hit-to-lead optimization identified a novel and selective PDE4 inhibitor 4e (IC 50 = 17 nM), which adopted a different binding pattern from PDE4 inhibitors roflumilast and rolipram. Oral administration of 4e at a dose of 10 mg/kg exhibited remarkable therapeutic effects in a VaD model and did not cause emesis to beagle dogs, indicating its potential as a novel anti-VaD agent.


  • Organizational Affiliation

    School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A, B
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
M36 (Subject of Investigation/LOI)
Query on M36

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
7-[8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-5-oxidanyl-6-oxidanylidene-pyrano[3,2-b]xanthen-9-yl]oxyheptanoic acid
C31 H36 O8
QHLZYKWHQKCZMD-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
M36 BindingDB:  6KK0 IC50: min: 8, max: 19 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.365α = 90
b = 77.984β = 90
c = 163.344γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21877134
National Natural Science Foundation of ChinaChina81522041
National Natural Science Foundation of ChinaChina21572279

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2020-05-13
    Changes: Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description