6FRD

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-637


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-637

Singh, A.K.Brown, D.G.

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
E3Q (Subject of Investigation/LOI)
Query on E3Q

Download Ideal Coordinates CCD File 
P [auth B]1-cycloheptyl-3-{4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl}-4,4-dimethyl-4,5-dihydro- 1H-pyrazol-5-one
C27 H34 N2 O4
KQFIOHKLWWEPIB-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

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E [auth A], F [auth A], G [auth A], J [auth A], M [auth B], N [auth B], O [auth B]GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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H [auth A], I [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.98α = 90
b = 113.48β = 107.89
c = 68.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata 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: 2019-03-13
    Type: Initial release