5N0Y

hPAD4 crystal complex with AFM-30a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1021/acs.jmedchem.7b00274
  • Primary Citation of Related Structures:  
    5N0M, 5N0Y, 5N0Z, 5N1B

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-arginine deiminase type-4670Homo sapiensMutation(s): 3 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8FQ
Query on 8FQ

Download Ideal Coordinates CCD File 
H [auth A]~{N}-[(1~{S})-4-(2-fluoranylethanimidoylamino)-1-(4-methoxy-1-methyl-benzimidazol-2-yl)butyl]-3-oxidanylidene-1,2-dihydroisoindole-4-carboxamide
C24 H27 F N6 O3
DMTSALXYYYZIBF-INIZCTEOSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.556α = 90
b = 60.929β = 124.69
c = 115.656γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary