SMTL ID : 7ue6.1

PANK3 complex structure with compound PZ-3802

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: W.274, N.307, L.341, A.345, W.349 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.307, A:W.349 Water bridges: A:V.276 EDO.2: 7 residues within 4Å: Chain A: L.30, T.69, I.71, R.94, F.95, P.96 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.3: 6 residues within 4Å: Chain A: I.284, R.289 Chain B: L.227, S.231, C.236, E.237 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.289, A:R.289 Water bridges: A:K.286, B:E.237 EDO.8: 5 residues within 4Å: Chain B: W.274, N.307, L.341, A.345, W.349 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.307, B:W.349 Water bridges: B:V.276 EDO.9: 7 residues within 4Å: Chain B: L.30, T.69, I.71, R.94, F.95, P.96 Ligands: ANP.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94 EDO.10: 6 residues within 4Å: Chain A: L.227, S.231, C.236, E.237 Chain B: I.284, R.289 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.289, B:R.289 Water bridges: B:K.286, A:E.237

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

ACT.4: 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 ACT.11: 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 NDK: 6-(4-{[5-fluoro-6-(propan-2-yl)pyridin-3-yl]acetyl}piperazin-1-yl)pyridazine-3-carbonitrile(Non-covalent)

NDK.5: 22 residues within 4Å: Chain A: E.146, V.202, S.203, R.215, T.217, G.218, T.219, S.220 Chain B: V.258, I.261, Y.266, L.271, V.276, A.277, N.307, G.310, S.311, R.314, A.345, L.346, W.349 Ligands: ANP.6 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.258, B:I.261, B:Y.266, B:L.271 Hydrogen bonds: B:R.314, A:V.202, A:R.215, A:R.215 pi-Stacking: B:W.349 pi-Cation interactions: A:R.215 NDK.12: 22 residues within 4Å: Chain A: V.258, I.261, Y.266, L.271, V.276, A.277, N.307, G.310, S.311, R.314, A.345, L.346, W.349 Chain B: E.146, V.202, S.203, R.215, T.217, G.218, T.219, S.220 Ligands: ANP.13 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:V.202, B:R.215, B:R.215, A:R.314 pi-Cation interactions: B:R.215 Hydrophobic interactions: A:V.258, A:I.261, A:Y.266, A:L.271 pi-Stacking: A:W.349

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

ANP.6: 22 residues within 4Å: Chain A: G.27, G.28, T.29, L.30, K.32, E.146, I.198, G.199, S.200, G.201, G.223, G.224, F.239, E.240, G.329, N.330, F.331, R.333 Chain B: I.261 Ligands: EDO.2, NDK.5, MG.7 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, A:L.30, 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:K.32, A:K.32, A:E.146, A:N.197, A:N.197, A:N.197, A:N.197, A:G.199 Salt bridges: A:K.32 pi-Stacking: A:F.239 ANP.13: 22 residues within 4Å: Chain A: I.261 Chain B: G.27, G.28, T.29, L.30, K.32, E.146, I.198, G.199, S.200, G.201, G.223, G.224, F.239, E.240, G.329, N.330, F.331, R.333 Ligands: EDO.9, NDK.12, MG.14 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, B:L.30, 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:K.32, B:K.32, B:E.146, B:N.197, B:N.197, B:N.197, B:N.197, B:G.199 Salt bridges: B:K.32 pi-Stacking: B:F.239

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

MG.7: 1 residues within 4Å: Ligands: ANP.6 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: ANP.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tangallapally, R. et al., Development of Brain Penetrant Pyridazine Pantothenate Kinase Activators. J.Med.Chem. (2024)

Release Date

2023-04-05

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3

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