SMTL ID : 9b98.1

Crystal structure of the human PAD2 protein bound to small molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 4 residues within 4Å: Chain A: Y.237, H.258, K.261, F.271 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.237 Hydrogen bonds: A:K.261 Water bridges: A:H.258 Salt bridges: A:H.258 ACT.2: 7 residues within 4Å: Chain A: D.144, G.149, V.151, M.202, S.203, Q.204, H.383 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.144, A:V.151, A:Q.204 Hydrogen bonds: A:G.149, A:Q.204 Salt bridges: A:H.383 ACT.9: 4 residues within 4Å: Chain B: Y.237, H.258, K.261, F.271 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.237 Hydrogen bonds: B:K.261 Water bridges: B:H.258 Salt bridges: B:H.258 ACT.10: 7 residues within 4Å: Chain B: D.144, G.149, V.151, M.202, S.203, Q.204, H.383 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.144, B:V.151, B:Q.204 Hydrogen bonds: B:G.149, B:Q.204 Salt bridges: B:H.383

10 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.177, E.179, D.201, K.384, D.410 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.177, A:D.201, A:D.201, A:D.410, H2O.4 CA.4: 6 residues within 4Å: Chain A: N.175, D.177, E.179, D.187, D.198, D.201 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.5: 4 residues within 4Å: Chain A: D.187, D.190, K.192, 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.1 CA.6: 5 residues within 4Å: Chain A: D.144, D.146, D.148, V.150, E.152 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.144, A:D.148, A:V.150, A:E.152, H2O.3 CA.7: 5 residues within 4Å: Chain A: Q.371, E.375, F.429, L.432, E.433 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.375, A:F.429, A:L.432, A:E.433 CA.11: 5 residues within 4Å: Chain B: D.177, E.179, D.201, K.384, D.410 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.177, B:D.201, B:D.201, B:D.410, H2O.10 CA.12: 6 residues within 4Å: Chain B: N.175, D.177, E.179, D.187, D.198, D.201 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: 4 residues within 4Å: Chain B: D.187, D.190, K.192, 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.6, H2O.7 CA.14: 5 residues within 4Å: Chain B: D.144, D.146, D.148, V.150, E.152 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.144, B:D.148, B:V.150, B:E.152, H2O.9 CA.15: 5 residues within 4Å: Chain B: Q.371, E.375, F.429, L.432, E.433 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.375, B:F.429, B:L.432, B:E.433

2 x 01: (5P)-N,N-diethyl-2-fluoro-5-(2-[({1-[2-(methylamino)-2-oxoethyl]cyclohexyl}methyl)amino]-6-{methyl[1-(2-methyl-1-phenyl-1H-1,3-benzimidazole-5-carbonyl)piperidin-4-yl]amino}pyrimidin-4-yl)benzamide

01.8: 18 residues within 4Å: Chain A: F.456, P.457, L.458, S.459, Y.564, M.596, D.599, H.600 Chain B: Y.224, Y.257, L.294, Y.296, M.297, D.300, I.301, P.302, L.303, P.305 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Y.224, B:Y.257, B:L.294, B:I.301, B:P.302, A:F.456, A:F.456, A:P.457, A:Y.564, A:Y.564, A:H.600 Salt bridges: B:D.300 Hydrogen bonds: A:L.458 pi-Stacking: A:H.600 01.16: 18 residues within 4Å: Chain A: Y.224, Y.257, L.294, Y.296, M.297, D.300, I.301, P.302, L.303, P.305 Chain B: F.456, P.457, L.458, S.459, Y.564, M.596, D.599, H.600 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Y.224, A:Y.257, A:L.294, A:I.301, A:P.302, B:F.456, B:F.456, B:P.457, B:Y.564, B:Y.564, B:H.600 Hydrogen bonds: A:D.300, B:L.458, B:H.600 Salt bridges: A:D.300 pi-Stacking: B:H.600

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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