SMTL ID : 9b97.1

Crystal structure of the human PAD2 protein bound to small molecule

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 6 residues within 4Å: Chain A: S.455, F.456, E.482, L.483, W.571 Ligands: ACT.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.456, A:E.482 Hydrogen bonds: A:L.483 Water bridges: A:E.482 MPD.12: 6 residues within 4Å: Chain B: S.455, F.456, E.482, L.483, W.571 Ligands: ACT.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.456, B:E.482 Hydrogen bonds: B:L.483 Water bridges: B:E.482

2 x 01: (1P)-N~3'~-[(2S)-3-cyclohexyl-1-(methylamino)-1-oxopropan-2-yl]-N~3~,N~3~-diethyl-4-fluoro-5'-{[4-(4-phenylbutyl)piperazin-1-yl]methyl}[1,1'-biphenyl]-3,3'-dicarboxamide

01.2: 19 residues within 4Å: Chain A: F.456, P.457, L.458, S.459, Q.560, E.561, Y.564, M.596, H.600 Chain B: V.222, Y.224, Y.257, L.294, Y.296, M.297, I.301, P.302, L.303, P.305 19 PLIP interactions: 10 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:V.222, B:Y.224, B:Y.224, B:Y.257, B:Y.257, B:Y.257, B:L.294, B:L.294, B:I.301, B:P.302, A:F.456, A:F.456, A:P.457, A:L.458, A:Y.564, A:H.600 Hydrogen bonds: A:L.458, A:L.458 Water bridges: A:Y.564 01.13: 19 residues within 4Å: Chain A: V.222, Y.224, Y.257, L.294, Y.296, M.297, I.301, P.302, L.303, P.305 Chain B: F.456, P.457, L.458, S.459, Q.560, E.561, Y.564, M.596, H.600 19 PLIP interactions: 10 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:V.222, A:Y.224, A:Y.224, A:Y.257, A:Y.257, A:Y.257, A:L.294, A:L.294, A:I.301, A:P.302, B:F.456, B:F.456, B:P.457, B:L.458, B:Y.564, B:H.600 Hydrogen bonds: B:L.458, B:L.458 Water bridges: B:Y.484

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

ACT.3: 3 residues within 4Å: Chain A: Y.237, H.258, K.261 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.237 Hydrogen bonds: A:V.259, A:K.261 Salt bridges: A:H.258, A:K.261 ACT.4: 6 residues within 4Å: Chain A: D.144, G.149, M.202, S.203, Q.204, H.383 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.144 Hydrogen bonds: A:G.149, A:Q.204 Water bridges: A:Q.204 Salt bridges: A:H.383 ACT.5: 6 residues within 4Å: Chain A: S.454, S.455, F.456, P.457, R.463 Ligands: MPD.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.463 Hydrogen bonds: A:S.454, A:S.455 Salt bridges: A:R.463 ACT.6: 3 residues within 4Å: Chain A: R.469, K.473, E.482 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.482 Salt bridges: A:K.473 ACT.14: 3 residues within 4Å: Chain B: Y.237, H.258, K.261 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.237 Hydrogen bonds: B:V.259, B:K.261 Salt bridges: B:H.258, B:K.261 ACT.15: 6 residues within 4Å: Chain B: D.144, G.149, M.202, S.203, Q.204, H.383 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.144 Hydrogen bonds: B:G.149, B:Q.204 Water bridges: B:Q.204 Salt bridges: B:H.383 ACT.16: 6 residues within 4Å: Chain B: S.454, S.455, F.456, P.457, R.463 Ligands: MPD.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.463 Hydrogen bonds: B:S.454, B:S.455 Salt bridges: B:R.463 ACT.17: 3 residues within 4Å: Chain B: R.469, K.473, E.482 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.482 Salt bridges: B:K.473

10 x CA: CALCIUM ION(Non-covalent)

CA.7: 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:E.179, A:D.201, A:D.410, H2O.3 CA.8: 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.9: 4 residues within 4Å: Chain A: D.187, D.190, K.192, E.274 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.187, A:D.190, H2O.1, H2O.1, H2O.2 CA.10: 5 residues within 4Å: Chain A: D.144, D.146, D.148, V.150, E.152 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.144, A:D.146, A:D.148, A:D.148, A:E.152 CA.11: 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.18: 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:E.179, B:D.201, B:D.410, H2O.9 CA.19: 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.20: 4 residues within 4Å: Chain B: D.187, D.190, K.192, E.274 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.187, B:D.190, H2O.7, H2O.7, H2O.8 CA.21: 5 residues within 4Å: Chain B: D.144, D.146, D.148, V.150, E.152 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.144, B:D.146, B:D.148, B:D.148, B:E.152 CA.22: 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

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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