6FDW

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-356


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

TbrPDEB1 structure with inhibitor NPD-356

Salado, I.G.Moreno, C.Sakaine, G.Singh, A.K.Blaazer, A.R.Siderius, M.Matheeussen, A.Gul, S.Maes, L.Leurs, R.Brown, D.G.Augustyns, K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PhosphodiesteraseA, B360Trypanosoma bruceiMutation(s): 0 
Gene Names: PDEB1
EC: 3.1.4
UniProt
Find proteins for Q8WQX9 (Trypanosoma brucei)
Explore Q8WQX9 
Go to UniProtKB:  Q8WQX9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D62 (Subject of Investigation/LOI)
Query on D62

Download Ideal Coordinates CCD File 
C [auth A], H [auth B](4aS,8aR)-2-(1-{2-aminothieno[2,3-d]pyrimidin-4-yl}piperidin-4-yl)-4-(3,4- dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one
C27 H30 N6 O3 S
VRSCGUCAJHMOSB-RBUKOAKNSA-N
 Ligand Interaction
GOL
Query on GOL

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G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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D [auth A], I [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GAI
Query on GAI

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F [auth A]GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], J [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.69α = 90
b = 119.26β = 108.38
c = 67.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release