SMTL ID : 9b96.1

Crystal structure of the human PAD2 protein bound to inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

2 x 01: 1-({(2P)-1-{(1R)-1-(2-bromophenyl)-3-[5-(methanesulfonamido)-2-methylanilino]-3-oxopropyl}-2-[3-(4-chlorophenoxy)phenyl]-1H-1,3-benzimidazol-6-yl}methyl)-N-methyl-D-prolinamide

01.1: 18 residues within 4Å: Chain A: S.455, F.456, L.458, G.460, G.461, R.462, Y.484, W.571 Chain B: Y.224, Y.257, L.294, Y.296, A.298, Q.299, I.301, P.302, L.303, P.305 20 PLIP interactions: 9 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:F.456, A:L.458, A:R.462, A:Y.484, A:Y.484, B:Y.257, B:Y.257, B:L.294, B:P.302, B:L.303, B:P.305 pi-Stacking: A:F.456, A:Y.484, A:W.571, A:W.571, B:Y.224 Hydrogen bonds: B:L.303 Water bridges: B:Y.257 pi-Cation interactions: B:Y.257 Halogen bonds: B:L.303 01.8: 18 residues within 4Å: Chain A: Y.224, Y.257, L.294, Y.296, A.298, Q.299, I.301, P.302, L.303, P.305 Chain B: S.455, F.456, L.458, G.460, G.461, R.462, Y.484, W.571 19 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.456, B:L.458, B:R.462, B:Y.484, B:Y.484, A:Y.257, A:Y.257, A:L.294, A:P.302, A:L.303, A:P.305 pi-Stacking: B:F.456, B:Y.484, B:W.571, B:W.571, A:Y.224 Hydrogen bonds: A:L.303 pi-Cation interactions: A:Y.257 Halogen bonds: A:L.303

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: Y.237, H.258, V.259, V.260, K.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.261 Salt bridges: A:H.258 ACT.3: 5 residues within 4Å: Chain A: D.144, G.149, M.202, S.203, Q.204 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.144 Hydrogen bonds: A:G.149, A:Q.204 Water bridges: A:Q.204 ACT.9: 5 residues within 4Å: Chain B: Y.237, H.258, V.259, V.260, K.261 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.261 Salt bridges: B:H.258 ACT.10: 5 residues within 4Å: Chain B: D.144, G.149, M.202, S.203, Q.204 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.144 Hydrogen bonds: B:G.149, B:Q.204 Water bridges: B:Q.204

8 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.177, E.179, D.201 Ligands: CA.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.177, A:E.179, H2O.3, H2O.3, H2O.12 CA.5: 7 residues within 4Å: Chain A: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.4 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.6: 5 residues within 4Å: Chain A: D.187, D.190, K.192, D.198, E.274 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.187, A:D.190, A:K.192, H2O.1, H2O.2 CA.7: 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.3 CA.11: 4 residues within 4Å: Chain B: D.177, E.179, D.201 Ligands: CA.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.177, B:E.179, H2O.21, H2O.21, H2O.30 CA.12: 7 residues within 4Å: Chain B: N.175, D.177, E.179, D.187, D.198, D.201 Ligands: CA.11 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.177, B:E.179, B:D.187, B:D.198, B:D.201 CA.13: 5 residues within 4Å: Chain B: D.187, D.190, K.192, D.198, E.274 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.187, B:D.190, B:K.192, H2O.19, H2O.20 CA.14: 5 residues within 4Å: Chain B: D.144, D.146, D.148, V.150, E.152 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.144, B:D.146, B:D.148, B:V.150, B:E.152, H2O.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Byrnes, L.J. et al., Discovery, Characterization, and Structure of a Cell Active PAD2 Inhibitor Acting through a Novel Allosteric Mechanism. Acs Chem.Biol. (2024)

Release Date

2024-10-09

Peptides

Protein-arginine deiminase type-2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein-arginine deiminase type-2

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