SMTL ID : 9dpz.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 2.41 Å

Oligo State

monomer

Ligands

1 x 01: (2S)-2-amino-2-{1-[7-(4-bromophenyl)-5,6-dimethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl]piperidin-4-yl}-1-(pyrrolidin-1-yl)ethan-1-one

01.1: 19 residues within 4Å: Chain A: V.160, N.161, L.262, A.263, F.264, D.266, F.376, D.377, S.378, V.400, T.401, R.402, S.414, F.415, L.418, M.451, A.454, L.455, F.458 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.160, A:F.376, A:V.400, A:R.402, A:F.415, A:L.455, A:L.455 Hydrogen bonds: A:F.264 Water bridges: A:L.262 pi-Stacking: A:F.415, A:F.458, A:F.458

1 x 3YZ: [(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone(Non-covalent)

3YZ.2: 17 residues within 4Å: Chain A: D.358, V.477, H.479, D.481, E.482, F.523, I.526, E.588, A.589, F.590, F.591, P.592, N.593, N.596, F.642, Y.644, V.651 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.523, A:N.593, A:F.642, A:Y.644 Hydrogen bonds: A:D.481, A:N.593, A:N.596, A:V.651

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-4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein-arginine deiminase type-4

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