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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphodiesterase
A, B
360Trypanosoma 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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E3Q
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
ZN
Query on ZN

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

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E [auth A]
F [auth A]
G [auth A]
J [auth A]
M [auth B]
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
FMT
Query on FMT

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

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D [auth A],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description