6RB6

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-053


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 

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
  • Primary Citation of Related Structures:  

  • 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.,University of California, San Diego, School of Medicine, Department of Neuroscience, 9500 Gilman Drive La Jolla, CA 92093-0662, USA.,Scintillon Institute, 6868 Nancy Ridge Drive, San Diego CA-92117, USA.,School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK.,Laboratory for Microbiology, Parasitology and Hygiene, University of Antwerp, 2610 Wilrijk, Belgium.,Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphodiesterase
A, B
360Trypanosoma bruceiMutation(s): 0 
Gene Names: PDEB1
EC: 3.1.4.-
Find proteins for Q8WQX9 (Trypanosoma brucei)
Go to UniProtKB:  Q8WQX9
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GAI
Query on GAI

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A, B
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
JX2
Query on JX2

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Download CCD File 
A, B
3-[5-[(4~{a}~{R},8~{a}~{S})-3-cycloheptyl-4-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(furan-2-ylmethyl)prop-2-ynamide
C30 H33 N3 O4
LKXRSFQDUFXVGE-IZZNHLLZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 147.516α = 90.00
b = 115.070β = 109.39
c = 63.780γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references
  • Version 1.2: 2019-09-04
    Type: Data collection, Database references