SMTL ID : 9d2o.1

PANK3 complex structure with compound PZ-5351

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x 01: N-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}-3-fluorophenyl)ethanesulfonamide

01.1: 21 residues within 4Å: Chain A: G.201, V.202, S.203, R.215, T.217, G.218, T.219 Chain B: V.258, Y.262, Y.266, L.271, V.276, A.277, N.307, G.310, S.311, R.314, A.345, L.346, W.349 Ligands: ANP.3 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.258, B:L.271, B:A.277, B:A.345 Hydrogen bonds: B:R.314, A:R.215, A:R.215 pi-Stacking: B:W.349 pi-Cation interactions: A:R.215 01.7: 21 residues within 4Å: Chain A: V.258, Y.262, Y.266, L.271, V.276, A.277, N.307, G.310, S.311, R.314, A.345, L.346, W.349 Chain B: G.201, V.202, S.203, R.215, T.217, G.218, T.219 Ligands: ANP.9 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.258, A:L.271, A:A.277, A:A.345 Hydrogen bonds: A:R.314, B:R.215, B:R.215 pi-Stacking: A:W.349 pi-Cation interactions: B:R.215

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.2: 9 residues within 4Å: Chain A: D.25, L.150, N.197, G.329, E.362, G.363, Y.364, F.365, G.366 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.25, A:E.362, A:F.365, A:G.366 Water bridges: A:A.367 ACY.8: 9 residues within 4Å: Chain B: D.25, L.150, N.197, G.329, E.362, G.363, Y.364, F.365, G.366 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.362, B:F.365, B:G.366 Water bridges: B:A.367

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.3: 21 residues within 4Å: Chain A: G.27, G.28, T.29, L.30, K.32, G.199, S.200, G.201, G.223, G.224, L.227, F.239, E.240, G.329, N.330, F.331, R.333 Chain B: I.261 Ligands: 01.1, MG.4, EDO.5 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, A:T.29, A:L.30, A:K.32, A:R.94, A:G.199, A:S.200, A:S.200, A:G.201, A:G.223, A:E.240, A:N.330, A:N.330, A:F.331, A:R.333 Water bridges: A:E.146, A:E.146, A:E.146, A:N.197, A:N.197, A:G.199, A:G.199 Salt bridges: A:K.32 pi-Stacking: A:F.239 ANP.9: 21 residues within 4Å: Chain A: I.261 Chain B: G.27, G.28, T.29, L.30, K.32, G.199, S.200, G.201, G.223, G.224, L.227, F.239, E.240, G.329, N.330, F.331, R.333 Ligands: 01.7, MG.10, EDO.11 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, B:L.30, B:K.32, B:R.94, B:G.199, B:S.200, B:S.200, B:G.201, B:G.223, B:E.240, B:N.330, B:N.330, B:F.331, B:R.333 Water bridges: B:T.29, B:N.197, B:N.197, B:G.199, B:G.199 Salt bridges: B:K.32 pi-Stacking: B:F.239

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 1 residues within 4Å: Ligands: ANP.3 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ANP.9 No protein-ligand interaction detected (PLIP)

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: L.30, T.69, R.94, F.95 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.6: 6 residues within 4Å: Chain A: I.284, R.289 Chain B: L.227, S.231, C.236, E.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.289, A:R.289 Water bridges: A:K.286 EDO.11: 5 residues within 4Å: Chain B: L.30, T.69, R.94, F.95 Ligands: ANP.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94 EDO.12: 6 residues within 4Å: Chain A: L.227, S.231, C.236, E.237 Chain B: I.284, R.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.289, B:R.289 Water bridges: B:K.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yun, M. et al., 2-(4-aminophenyl)acetamide derivatives as Pantothenate Kinase Inhibitors. To Be Published

Release Date

2025-08-13

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3

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