6FE3

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1439


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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-1439

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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WQX9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D68
Query on D68

Download Ideal Coordinates CCD File 
E [auth A] 1-(2-{4-[(4aS,8aR)-4-[3,4-bis(difluoromethoxy)phenyl]-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)-4,4-dimethylpiperidine-2,6-dione
C30 H34 F4 N4 O6
WVAQTVIALKSAMT-VQTJNVASSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
O [auth B],
P [auth B],
Q [auth B],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
L [auth A],
M [auth A],
N [auth A],
C [auth A],
D [auth A],
L [auth A],
M [auth A],
N [auth A],
T [auth B],
U [auth B]
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.53α = 90
b = 114.82β = 108.25
c = 68.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

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