5TKB

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH A TETRAFLUORANLINE COMPOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of imidazo[1,2-b]pyridazine TYK2 pseudokinase ligands as potent and selective allosteric inhibitors of TYK2 signalling.

Moslin, R.Gardner, D.Santella, J.Zhang, Y.Duncia, J.V.Liu, C.Lin, J.Tokarski, J.S.Strnad, J.Pedicord, D.Chen, J.Blat, Y.Zupa-Fernandez, A.Cheng, L.Sun, H.Chaudhry, C.Huang, C.D'Arienzo, C.Sack, J.S.Muckelbauer, J.K.Chang, C.Tredup, J.Xie, D.Aranibar, N.Burke, J.R.Carter, P.H.Weinstein, D.S.

(2017) Medchemcomm 8: 700-712


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A, B, C, D
381Homo sapiensMutation(s): 2 
Gene Names: PDE4D (DPDE3)
EC: 3.1.4.53
Find proteins for Q08499 (Homo sapiens)
Go to Gene View: PDE4D
Go to UniProtKB:  Q08499
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
7DJ
Query on 7DJ

Download SDF File 
Download CCD File 
A, B, C, D
N-[(2R)-2,3-dihydroxy-2-methylpropyl]-8-(methylamino)-6-[(2,3,5,6-tetrafluorophenyl)amino]imidazo[1,2-b]pyridazine-3-carboxamide
C18 H18 F4 N6 O3
HNSFAKGAIZARCR-GOSISDBHSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A, B, C, D
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.000α = 90.00
b = 112.700β = 90.00
c = 159.880γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
BUSTERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-10-06 
  • Released Date: 2016-12-28 
  • Deposition Author(s): Sack, J.S.

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references