4X8G

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK199


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4X8C, 4X8G

  • 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 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 ...

    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

    1] EpiNova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline,Medicines Research Centre, Stevenage, Hertfordshire, UK. [2] AstraZeneca, Oncology iMed, Cambridge Science Park, Cambridge, UK (R.J.S. and D.M.W.); Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA (D.J.S.); University of Massachussetts Medical School, Worcester, Massachusetts, USA (P.R.T.).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-arginine deiminase type-4A671Homo sapiensMutation(s): 1 
Gene Names: PADI4PADI5PDI5PAD4
EC: 3.5.3.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM07 (Homo sapiens)
Explore Q9UM07 
Go to UniProtKB:  Q9UM07
PHAROS:  Q9UM07
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM07
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3Z0
Query on 3Z0

Download Ideal Coordinates CCD File 
F [auth A][(3R)-3-aminopiperidin-1-yl][2-(1-ethyl-1H-pyrrolo[2,3-b]pyridin-2-yl)-7-methoxy-1-methyl-1H-benzimidazol-5-yl]methanone
C24 H28 N6 O2
JCCVZBCVMBEDEN-QGZVFWFLSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.99α = 90
b = 62.25β = 124.71
c = 116.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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