6RCW

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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:  
    6GXQ, 6HWO, 6RB6, 6RCW, 6RFW, 6RFN, 6RGK

  • 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 activities against TbrPDEB1 and anti-T ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4DA, B, C, D364Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JX2
Query on JX2

Download Ideal Coordinates CCD File 
GB [auth D], HA [auth B], RA [auth C]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
EPE
Query on EPE

Download Ideal Coordinates CCD File 
GA [auth B], QA [auth C]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

Download Ideal Coordinates CCD File 
SA [auth D], T [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
FB [auth D], HB [auth D], S [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], IA [auth C], TA [auth D], U [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , AB [auth D] , BA [auth B] , BB [auth D] , CA [auth B] , CB [auth D] , DA [auth B] , DB [auth D] , 
AA [auth B],  AB [auth D],  BA [auth B],  BB [auth D],  CA [auth B],  CB [auth D],  DA [auth B],  DB [auth D],  EA [auth B],  EB [auth D],  FA [auth B],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  KA [auth C],  L [auth A],  LA [auth C],  M [auth A],  MA [auth C],  N [auth A],  NA [auth C],  O [auth A],  OA [auth C],  P [auth A],  PA [auth C],  Q [auth A],  R [auth A],  VA [auth D],  W [auth B],  WA [auth D],  X [auth B],  XA [auth D],  Y [auth B],  YA [auth D],  Z [auth B],  ZA [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A], JA [auth C], UA [auth D], V [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.894α = 90
b = 110.505β = 90
c = 160.694γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union602666

Revision History  (Full details and data files)

  • 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