6HWO

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1335


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2).

de Heuvel, E.Singh, A.K.Boronat, P.Kooistra, A.J.van der Meer, T.Sadek, P.Blaazer, A.R.Shaner, N.C.Bindels, D.S.Caljon, G.Maes, L.Sterk, G.J.Siderius, M.Oberholzer, M.de Esch, I.J.P.Brown, D.G.Leurs, R.

(2019) Bioorg Med Chem 27: 4013-4029

  • DOI: 10.1016/j.bmc.2019.06.026
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Inhibitors against Trypanosoma brucei phosphodiesterase B1 (TbrPDEB1) and B2 (TbrPDEB2) have gained interest as new treatments for human African trypanosomiasis. The recently reported alkynamide tetrahydrophthalazinones, which show submicromolar acti ...

    Inhibitors against Trypanosoma brucei phosphodiesterase B1 (TbrPDEB1) and B2 (TbrPDEB2) have gained interest as new treatments for human African trypanosomiasis. The recently reported alkynamide tetrahydrophthalazinones, which show submicromolar activities against TbrPDEB1 and anti-T. brucei activity, have been used as starting point for the discovery of new TbrPDEB1 inhibitors. Structure-based design indicated that the alkynamide-nitrogen atom can be readily decorated, leading to the discovery of 37, a potent TbrPDEB1 inhibitor with submicromolar activities against T. brucei parasites. Furthermore, 37 is more potent against TbrPDEB1 than hPDE4 and shows no cytotoxicity on human MRC-5 cells. The crystal structures of the catalytic domain of TbrPDEB1 co-crystalized with several different alkynamides show a bidentate interaction with key-residue Gln874, but no interaction with the parasite-specific P-pocket, despite being (uniquely) a more potent inhibitor for the parasite PDE. Incubation of blood stream form trypanosomes by 37 increases intracellular cAMP levels and results in the distortion of the cell cycle and cell death, validating phosphodiesterase inhibition as mode of action.


    Organizational Affiliation

    Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands. Electronic address: r.leurs@vu.nl.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A, B, C, D
364Homo sapiensMutation(s): 0 
Gene Names: PDE4DDPDE3
EC: 3.1.4.53
Find proteins for Q08499 (Homo sapiens)
Go to UniProtKB:  Q08499
NIH Common Fund Data Resources
PHAROS  Q08499
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FFZ
Query on FFZ

Download CCD File 
A, B, C, D
3-[5-[(4aR,8aS)-4-OXIDANYLIDENE-3-PROPAN-2-YL-4a,5,8,8a-TETRAHYDROPHTHALAZIN-1-YL]-2-METHOXY-PHENYL]-N-(PHENYLMETHYL)PROP-2-YNAMIDE
C28 H29 N3 O3
CNKULZYKNGMIIR-BJKOFHAPSA-N
 Ligand Interaction
EPE
Query on EPE

Download CCD File 
A, B, C, D
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A, B, C, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
B, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.465α = 90
b = 110.848β = 90
c = 160.461γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union602666

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Database references