SMTL ID : 9dol.1

Potent inhibition of the protein arginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.177, E.179, D.201, K.384, D.410 Ligands: CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.177, A:E.179, A:D.201, A:D.410, H2O.3 CA.2: 7 residues within 4Å: Chain A: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.177, A:E.179, A:D.187, A:D.198, A:D.201 CA.3: 3 residues within 4Å: Chain A: D.187, D.190, K.192 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.187, A:D.190, A:K.192, H2O.1, H2O.4, H2O.10 CA.4: 5 residues within 4Å: Chain A: D.144, D.146, D.148, V.150, E.152 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.144, A:D.146, A:D.148, A:V.150, A:E.152, H2O.4

1 x 01: (2S)-2-amino-2-{1-[(5M)-5-(3,5-dichloropyridin-2-yl)isoquinolin-1-yl]piperidin-4-yl}-1-(pyrrolidin-1-yl)ethan-1-one

01.5: 23 residues within 4Å: Chain A: V.174, C.176, E.186, C.188, R.189, L.276, C.277, F.278, D.280, L.390, D.391, S.392, V.414, T.415, R.416, E.417, S.428, F.429, L.432, M.464, V.467, V.468, F.471 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.186, A:L.390, A:L.390, A:V.414, A:R.416, A:V.468, A:V.468 Hydrogen bonds: A:F.278, A:S.392, A:R.416 Water bridges: A:D.280, A:D.280, A:E.417, A:E.417 pi-Stacking: A:F.429

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dakin, L.A. et al., Inhibiting peptidylarginine deiminases (PAD1-4) by targeting a Ca 2+ dependent allosteric binding site. Nat Commun (2025)

Release Date

2025-05-28

Peptides

Protein-arginine deiminase type-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein-arginine deiminase type-2

Related Entries With Identical Sequence