4X8C

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK147


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation.

Lewis, H.D.Liddle, J.Coote, J.E.Atkinson, S.J.Barker, M.D.Bax, B.D.Bicker, K.L.Bingham, R.P.Campbell, M.Chen, Y.H.Chung, C.W.Craggs, P.D.Davis, R.P.Eberhard, D.Joberty, G.Lind, K.E.Locke, K.Maller, C.Martinod, K.Patten, C.Polyakova, O.Rise, C.E.Rudiger, M.Sheppard, R.J.Slade, D.J.Thomas, P.Thorpe, J.Yao, G.Drewes, G.Wagner, D.D.Thompson, P.R.Prinjha, R.K.Wilson, D.M.

(2015) Nat.Chem.Biol. 11: 189-191

  • DOI: 10.1038/nchembio.1735
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PAD4 has been strongly implicated in the pathogenesis of autoimmune, cardiovascular and oncological diseases through clinical genetics and gene disruption in mice. New selective PAD4 inhibitors binding a calcium-deficient form of the PAD4 enzyme have ...

    PAD4 has been strongly implicated in the pathogenesis of autoimmune, cardiovascular and oncological diseases through clinical genetics and gene disruption in mice. New selective PAD4 inhibitors binding a calcium-deficient form of the PAD4 enzyme have validated the critical enzymatic role of human and mouse PAD4 in both histone citrullination and neutrophil extracellular trap formation for, to our knowledge, the first time. The therapeutic potential of PAD4 inhibitors can now be explored.


    Organizational Affiliation

    EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-arginine deiminase type-4
A
671Homo sapiensMutation(s): 1 
Gene Names: PADI4 (PAD4, PADI5, PDI5)
EC: 3.5.3.15
Find proteins for Q9UM07 (Homo sapiens)
Go to Gene View: PADI4
Go to UniProtKB:  Q9UM07
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
3YZ
Query on 3YZ

Download SDF File 
Download CCD File 
A
[(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone
C26 H30 N6 O3
SHBUAYSOPVZNDD-GHTZIAJQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.500α = 90.00
b = 60.420β = 123.13
c = 113.310γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
BUSTERrefinement
Aimlessdata scaling
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references
  • Version 1.2: 2015-02-25
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Data collection, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.4: 2018-04-18
    Type: Data collection