Crystal structure of human phosphodiesterase 4B catalytic domain with inhibitor NPD-001

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity.

Blaazer, A.R.Singh, A.K.de Heuvel, E.Edink, E.Orrling, K.M.Veerman, J.J.N.van den Bergh, T.Jansen, C.Balasubramaniam, E.Mooij, W.J.Custers, H.Sijm, M.Tagoe, D.N.A.Kalejaiye, T.D.Munday, J.C.Tenor, H.Matheeussen, A.Wijtmans, M.Siderius, M.de Graaf, C.Maes, L.de Koning, H.P.Bailey, D.S.Sterk, G.J.de Esch, I.J.P.Brown, D.G.Leurs, R.

(2018) J Med Chem 61: 3870-3888

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01670
  • Primary Citation of Related Structures:  
    5G2B, 5G57, 5G5V, 5L8C, 5L8Y, 5L9H, 5LAQ, 5LBO

  • PubMed Abstract: 

    Several trypanosomatid cyclic nucleotide phosphodiesterases (PDEs) possess a unique, parasite-specific cavity near the ligand-binding region that is referred to as the P-pocket. One of these enzymes, Trypanosoma brucei PDE B1 (TbrPDEB1), is considered a drug target for the treatment of African sleeping sickness. Here, we elucidate the molecular determinants of inhibitor binding and reveal that the P-pocket is amenable to directed design. By iterative cycles of design, synthesis, and pharmacological evaluation and by elucidating the structures of inhibitor-bound TbrPDEB1, hPDE4B, and hPDE4D complexes, we have developed 4a,5,8,8a-tetrahydrophthalazinones as the first selective TbrPDEB1 inhibitor series. Two of these, 8 (NPD-008) and 9 (NPD-039), were potent ( K i = 100 nM) TbrPDEB1 inhibitors with antitrypanosomal effects (IC 50 = 5.5 and 6.7 μM, respectively). Treatment of parasites with 8 caused an increase in intracellular cyclic adenosine monophosphate (cAMP) levels and severe disruption of T. brucei cellular organization, chemically validating trypanosomal PDEs as therapeutic targets in trypanosomiasis.

  • Organizational Affiliation

    Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , 1081 HZ Amsterdam , The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B,cAMP-specific 3',5'-cyclic phosphodiesterase 4B421Homo sapiensMutation(s): 0 
Gene Names: PDE4BDPDE4
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens)
Explore Q07343 
Go to UniProtKB:  Q07343
PHAROS:  Q07343
GTEx:  ENSG00000184588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07343
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6M5

Download Ideal Coordinates CCD File 
F [auth A](4~{a}~{S},8~{a}~{R})-2-cycloheptyl-4-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy]phenyl]-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one
C33 H40 N6 O4
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth A]
C2 H3 O2
Query on MG

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
6M5 BindingDB:  5LAQ Ki: 0.63 (nM) from 1 assay(s)
IC50: min: 0.5, max: 0.63 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.737α = 90
b = 95.737β = 90
c = 85.113γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.3: 2019-04-24
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description