SMTL ID : 7uet.1

PANK3 complex structure with compound PZ-4140

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MXW: N-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}phenyl)methanesulfonamide(Non-covalent)

MXW.1: 22 residues within 4Å: Chain A: E.146, G.201, V.202, R.215, T.217, G.218, T.219 Chain B: V.258, 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.2 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.215, A:R.215, B:R.314 Water bridges: A:G.201 pi-Cation interactions: A:R.215 Hydrophobic interactions: B:V.258, B:L.271, B:A.277, B:A.345 pi-Stacking: B:W.349 MXW.6: 22 residues within 4Å: Chain A: V.258, 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, R.215, T.217, G.218, T.219 Ligands: ANP.7 10 PLIP interactions: 6 interactions with chain A, 4 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 Water bridges: B:G.201 pi-Cation interactions: B:R.215

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

ANP.2: 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: MXW.1, EDO.3, MG.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, A:L.30, A:K.32, A:R.94, A:G.199, 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: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.7: 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: MXW.6, EDO.8, MG.10 24 PLIP interactions: 24 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: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:N.197, B:N.197, B:N.197, B:N.197, B:G.199 Salt bridges: B:K.32 pi-Stacking: B:F.239

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

EDO.3: 6 residues within 4Å: Chain A: L.30, T.69, I.71, R.94, F.95 Ligands: ANP.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.94 Water bridges: A:E.240 EDO.4: 5 residues within 4Å: Chain A: D.265, Y.266, E.267, R.268 Chain B: Y.127 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.265, A:E.267, A:R.268 Water bridges: B:Y.127 EDO.8: 6 residues within 4Å: Chain B: L.30, T.69, I.71, R.94, F.95 Ligands: ANP.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.94 Water bridges: B:E.240 EDO.9: 5 residues within 4Å: Chain A: Y.127 Chain B: D.265, Y.266, E.267, R.268 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.265, B:E.267, B:R.268

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

MG.5: 1 residues within 4Å: Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ANP.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tangallapally, R. et al., Discovery of hPANK Activators with Improved Pharmacological Properties. To Be Published

Release Date

2023-03-29

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3

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