8GOD

Co-crystal structure of Human Protein-arginine deiminase type-4 (PAD4) with small molecule inhibitor JBI-589


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Alleviation of arthritis through prevention of neutrophil extracellular traps by an orally available inhibitor of protein arginine deiminase 4.

Gajendran, C.Fukui, S.Sadhu, N.M.Zainuddin, M.Rajagopal, S.Gosu, R.Gutch, S.Fukui, S.Sheehy, C.E.Chu, L.Vishwakarma, S.Jeyaraj, D.A.Hallur, G.Wagner, D.D.Sivanandhan, D.

(2023) Sci Rep 13: 3189-3189

  • DOI: https://doi.org/10.1038/s41598-023-30246-2
  • Primary Citation of Related Structures:  
    8GOD

  • PubMed Abstract: 

    Protein arginine deiminases (PAD) 4 is an enzyme that catalyzes citrullination of protein and its role in autoimmune diseases has been established through clinical genetics and gene knock out studies in mice. Further, studies with PAD4 - deficient mice have shown that PAD4 deficiency does not lead to increased infection or immune suppression, which makes PAD4 an attractive therapeutic target for auto-immune and inflammatory diseases. PAD4 has critical enzymatic role of promoting chromatin decondensation and neutrophil extracellular traps (NETs) formation that is associated with a number of immune-mediated pathological conditions. Here, we present a non-covalent PAD4 inhibitor JBI-589 with high PAD4 isoform selectivity and delineated its binding mode at 2.88 Å resolution by X-ray crystallography. We confirmed its effectiveness in inhibiting NET formation in vitro. Additionally, by using two mouse arthritis models for human rheumatoid arthritis (RA), the well-known disease associated with PAD4 clinically, we established its efficacy in vivo. These results suggest that JBI-589 would be beneficial for both PAD4 and NET-associated pathological conditions.


  • Organizational Affiliation

    Jubilant Therapeutics Inc., Bedminster, NJ, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-arginine deiminase type-4691Homo sapiensMutation(s): 0 
Gene Names: PADI4PAD4PADI5PDI5
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
GTEx:  ENSG00000159339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM07
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K3X (Subject of Investigation/LOI)
Query on K3X

Download Ideal Coordinates CCD File 
B [auth A][(3~{R})-3-azanylpiperidin-1-yl]-[2-[1-[(4-fluorophenyl)methyl]indol-2-yl]-3-methyl-imidazo[1,2-a]pyridin-7-yl]methanone
C29 H28 F N5 O
DUVCPNSLXBKGOK-XMMPIXPASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
K3X BindingDB:  8GOD IC50: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.456α = 90
b = 60.879β = 104.585
c = 127.097γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description