5N0M

hPAD4 crystal complex with BB-F-amidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Development of a Selective Inhibitor of Protein Arginine Deiminase 2.

Muth, A.Subramanian, V.Beaumont, E.Nagar, M.Kerry, P.McEwan, P.Srinath, H.Clancy, K.Parelkar, S.Thompson, P.R.

(2017) J. Med. Chem. 60: 3198-3211

  • DOI: 10.1021/acs.jmedchem.7b00274
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein arginine deiminase 2 (PAD2) plays a key role in the onset and progression of multiple sclerosis, rheumatoid arthritis, and breast cancer. To date, no PAD2-selective inhibitor has been developed. Such a compound will be critical for elucidatin ...

    Protein arginine deiminase 2 (PAD2) plays a key role in the onset and progression of multiple sclerosis, rheumatoid arthritis, and breast cancer. To date, no PAD2-selective inhibitor has been developed. Such a compound will be critical for elucidating the biological roles of this isozyme and may ultimately be useful for treating specific diseases in which PAD2 activity is dysregulated. To achieve this goal, we synthesized a series of benzimidazole-based derivatives of Cl-amidine, hypothesizing that this scaffold would allow access to a series of PAD2-selective inhibitors with enhanced cellular efficacy. Herein, we demonstrate that substitutions at both the N-terminus and C-terminus of Cl-amidine result in >100-fold increases in PAD2 potency and selectivity (30a, 41a, and 49a) as well as cellular efficacy (30a). Notably, these compounds use the far less reactive fluoroacetamidine warhead. In total, we predict that 30a will be a critical tool for understanding cellular PAD2 function and sets the stage for treating diseases in which PAD2 activity is dysregulated.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , 364 Plantation Street, Worcester, Massachusetts 01605, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-arginine deiminase type-4
A
670Homo sapiensMutation(s): 3 
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 3 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
8HT
Query on 8HT

Download SDF File 
Download CCD File 
A
~{N}-[(1~{S})-1-(1~{H}-benzimidazol-2-yl)-4-(2-fluoranylethanimidoylamino)butyl]-4-phenyl-benzamide
C26 H26 F N5 O
YLSHDLCSANAKPH-QHCPKHFHSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 147.910α = 90.00
b = 61.300β = 124.83
c = 115.750γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XSCALEdata scaling
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesGM079357 - GM110394 - GM118112

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release