SMTL ID : 9ecg.1

PANK3 complex structure with compound PZ-5588

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: L.30, T.69, R.94, F.95, P.96 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.2: 6 residues within 4Å: Chain A: I.284, R.289 Chain B: L.227, S.231, C.236, E.237 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.289, A:R.289, B:S.231 Water bridges: A:I.284, A:K.286 EDO.7: 6 residues within 4Å: Chain B: L.30, T.69, R.94, F.95, P.96 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94 EDO.8: 6 residues within 4Å: Chain A: L.227, S.231, C.236, E.237 Chain B: I.284, R.289 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.289, B:R.289, A:S.231 Water bridges: B:I.284, B:K.286

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

01.3: 22 residues within 4Å: Chain A: E.146, G.201, V.202, S.203, R.215, G.218, T.219, S.220 Chain B: I.261, 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.4 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.215, A:R.215, B:R.314 Water bridges: A:G.28, A:G.201 pi-Cation interactions: A:R.215 Hydrophobic interactions: B:Y.266, B:L.271, B:A.277, B:A.345 pi-Stacking: B:W.349 01.9: 22 residues within 4Å: Chain A: I.261, 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: E.146, G.201, V.202, S.203, R.215, G.218, T.219, S.220 Ligands: ANP.10 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.266, 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 Water bridges: B:G.28, B:G.201 pi-Cation interactions: B:R.215

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

ANP.4: 21 residues within 4Å: Chain A: G.27, G.28, T.29, L.30, K.32, 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.1, 01.3, MG.5 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, A:L.30, A:L.30, A:K.32, 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:R.333 Water bridges: A:K.32, 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.10: 21 residues within 4Å: Chain A: I.261 Chain B: G.27, G.28, T.29, L.30, K.32, 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.7, 01.9, MG.11 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, B:L.30, B:L.30, B:K.32, 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:R.333 Water bridges: B:T.29, B:K.32, B:E.146, B:E.146, 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.5: 1 residues within 4Å: Ligands: ANP.4 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: ANP.10 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: L.141, H.142, K.143 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: L.141, H.142, K.143 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tangallapally, R. et al., Isoform Selectivity Driven Pantothenate Kinases Activation by Novel Sulfonamide Analogues of Pantazines. To Be Published

Release Date

2025-11-19

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3

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