SMTL ID : 9ovq.1

PAD2 with an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x 01: (2S)-2-amino-2-(1-{(5M)-5-[3,5-dichloro-6-(1-methyl-1H-pyrazol-3-yl)pyridin-2-yl]isoquinolin-1-yl}piperidin-4-yl)-N-methylacetamide

01.1: 22 residues within 4Å: Chain A: V.161, E.173, C.175, L.263, C.264, F.265, D.267, D.359, L.377, D.378, S.379, V.401, T.402, R.403, V.410, D.414, S.415, F.416, L.419, V.454, V.455, F.458 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.377, A:V.401, A:R.403, A:F.416, A:V.455, A:V.455 Hydrogen bonds: A:F.265, A:S.379 pi-Stacking: A:F.416

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: N.162, D.164, E.166, D.174, D.185, D.188 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.166, A:D.174, A:D.185, A:D.188 CA.3: 4 residues within 4Å: Chain A: D.174, D.177, K.179, D.185 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.174, A:D.185, H2O.1 CA.4: 5 residues within 4Å: Chain A: D.164, E.166, D.188, K.371, D.397 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.164, A:E.166, A:D.188, H2O.1 CA.5: 5 residues within 4Å: Chain A: D.131, D.133, D.135, V.137, E.139 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.131, A:D.133, A:D.135, A:V.137, A:E.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schnute, M.E. et al., Peptidylarginine Deiminase (PAD) Inhibitor Optimization through Displacement of a Trapped Water Molecule. Acs Med.Chem.Lett. (2025)

Release Date

2025-07-30

Peptides

Protein-arginine deiminase type-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein-arginine deiminase type-2