4Z2B

The structure of human PDE12 residues 161-609 in complex with GSK3036342A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors.

Wood, E.R.Bledsoe, R.Chai, J.Daka, P.Deng, H.Ding, Y.Harris-Gurley, S.Kryn, L.H.Nartey, E.Nichols, J.Nolte, R.T.Prabhu, N.Rise, C.Sheahan, T.Shotwell, J.B.Smith, D.Tai, V.Taylor, J.D.Tomberlin, G.Wang, L.Wisely, B.You, S.Xia, B.Dickson, H.

(2015) J.Biol.Chem. 290: 19681-19696

  • DOI: 10.1074/jbc.M115.653113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 2',5'-Oligoadenylate synthetase (OAS) enzymes and RNase-L constitute a major effector arm of interferon (IFN)-mediated antiviral defense. OAS produces a unique oligonucleotide second messenger, 2',5'-oligoadenylate (2-5A), that binds and activates RN ...

    2',5'-Oligoadenylate synthetase (OAS) enzymes and RNase-L constitute a major effector arm of interferon (IFN)-mediated antiviral defense. OAS produces a unique oligonucleotide second messenger, 2',5'-oligoadenylate (2-5A), that binds and activates RNase-L. This pathway is down-regulated by virus- and host-encoded enzymes that degrade 2-5A. Phosphodiesterase 12 (PDE12) was the first cellular 2-5A- degrading enzyme to be purified and described at a molecular level. Inhibition of PDE12 may up-regulate the OAS/RNase-L pathway in response to viral infection resulting in increased resistance to a variety of viral pathogens. We generated a PDE12-null cell line, HeLaΔPDE12, using transcription activator-like effector nuclease-mediated gene inactivation. This cell line has increased 2-5A levels in response to IFN and poly(I-C), a double-stranded RNA mimic compared with the parental cell line. Moreover, HeLaΔPDE12 cells were resistant to viral pathogens, including encephalomyocarditis virus, human rhinovirus, and respiratory syncytial virus. Based on these results, we used DNA-encoded chemical library screening to identify starting points for inhibitor lead optimization. Compounds derived from this effort raise 2-5A levels and exhibit antiviral activity comparable with the effects observed with PDE12 gene inactivation. The crystal structure of PDE12 complexed with an inhibitor was solved providing insights into the structure-activity relationships of inhibitor potency and selectivity.


    Organizational Affiliation

    From the Departments of Biological Sciences and edgar.r.wood@mindspring.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2',5'-phosphodiesterase 12
A
455Homo sapiensMutation(s): 0 
Gene Names: PDE12
EC: 3.1.4.-
Find proteins for Q6L8Q7 (Homo sapiens)
Go to Gene View: PDE12
Go to UniProtKB:  Q6L8Q7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
4LC
Query on 4LC

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Download CCD File 
A
3-(6-{[(2S,3S)-3-(hydroxymethyl)-2-phenylmorpholin-4-yl]carbonyl}-1-methyl-1H-benzimidazol-2-yl)-1H-indole-6-carbonitrile
C29 H25 N5 O3
BFUYKHPXWBXKQQ-SVBPBHIXSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4LCKi: 17.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.309α = 90.00
b = 66.532β = 90.00
c = 124.880γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALEPACKdata scaling
PHASERphasing
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-06-24
    Type: Database references
  • Version 1.2: 2015-08-19
    Type: Database references