5LAQ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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This is version 1.3 of the entry. See complete history. 


Literature

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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B,cAMP-specific 3',5'-cyclic phosphodiesterase 4BA421Homo sapiensMutation(s): 0 
Gene Names: PDE4B, DPDE4
EC: 3.1.4.53
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens)
Explore Q07343 
Go to UniProtKB:  Q07343
PHAROS:  Q07343
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07343
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6M5
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
DNDNLFXKQSTINI-WUFINQPMSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth A]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6M5 Binding MOAD:  5LAQ Ki: 0.63 (nM) from 1 assay(s)
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

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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