Crystal structure of human peptidylarginine deiminase 4 in complex with o-Cl-amidine

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

Starting Model: experimental
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The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl-amidine) As Second Generation Protein Arginine Deiminase (PAD) Inhibitors

Causey, C.P.Jones, J.E.Slack, J.L.Kamei, D.Jones Jr, L.E.Subramanian, V.Knuckley, B.Ebrahimi, P.Chumanevich, A.A.Luo, Y.Hashimoto, H.Sato, M.Hofseth, L.J.Thompson, P.R.

(2011) J Med Chem 54: 6919-6935

  • DOI: https://doi.org/10.1021/jm2008985
  • Primary Citation of Related Structures:  
    3B1T, 3B1U

  • PubMed Abstract: 

    Protein arginine deiminase (PAD) activity is upregulated in a number of human diseases, including rheumatoid arthritis, ulcerative colitis, and cancer. These enzymes, there are five in humans (PADs 1-4 and 6), regulate gene transcription, cellular differentiation, and the innate immune response. Building on our successful generation of F- and Cl-amidine, which irreversibly inhibit all of the PADs, a structure-activity relationship was performed to develop second generation compounds with improved potency and selectivity. Incorporation of a carboxylate ortho to the backbone amide resulted in the identification of N-α-(2-carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine amide (o-F-amidine) and N-α-(2-carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine amide (o-Cl-amidine), as PAD inactivators with improved potency (up to 65-fold) and selectivity (up to 25-fold). Relative to F- and Cl-amidine, the compounds also show enhanced potency in cellulo. As such, these compounds will be versatile chemical probes of PAD function.

  • Organizational Affiliation

    Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-arginine deiminase type-4671Homo sapiensMutation(s): 0 
Gene Names: PADI4PADI5PDI5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM07 (Homo sapiens)
Explore Q9UM07 
Go to UniProtKB:  Q9UM07
GTEx:  ENSG00000159339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM07
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on YCL

Download Ideal Coordinates CCD File 
B [auth A]2-{[(2S)-1-amino-5-{[(1Z)-2-chloroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid
C15 H19 Cl N4 O4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
O4 S
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
YCL PDBBind:  3B1T IC50: 2200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.787α = 90
b = 60.853β = 123.99
c = 114.302γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description