SMTL ID : 7uey.1

PANK3 complex structure with compound PZ-4128

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 23 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, L.227, F.239, E.240, G.329, N.330, F.331, R.333 Chain B: I.261 Ligands: N0R.3, MG.4, EDO.6 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, 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:F.331, A:R.333 Water bridges: A:E.146, A:N.197, A:N.197, A:G.199, A:R.333, A:G.363 Salt bridges: A:K.32 pi-Stacking: A:F.239 ANP.2: 5 residues within 4Å: Chain A: R.134, L.141, H.142, K.143 Ligands: MG.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.134, A:H.142, A:K.143, A:K.143 Salt bridges: A:H.142 ANP.10: 23 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, L.227, F.239, E.240, G.329, N.330, F.331, R.333 Ligands: N0R.12, MG.13, EDO.15 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, 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:F.331, B:R.333 Water bridges: B:T.29, B:N.197, B:N.197, B:G.199, B:R.333, B:G.363 Salt bridges: B:K.32 pi-Stacking: B:F.239 ANP.11: 5 residues within 4Å: Chain B: R.134, L.141, H.142, K.143 Ligands: MG.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.134, B:L.141, B:H.142, B:K.143, B:K.143 Salt bridges: B:H.142

2 x N0R: N-(4-{2-[4-(6-chloropyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}phenyl)-2-hydroxyacetamide(Non-covalent)

N0R.3: 22 residues within 4Å: Chain A: E.146, G.201, V.202, R.215, T.217, G.218, T.219, S.220 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.1 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.258, B:L.271, B:A.345 Hydrogen bonds: B:R.314, A:E.146, A:G.201, A:R.215, A:R.215 pi-Stacking: B:W.349 Water bridges: A:E.146 pi-Cation interactions: A:R.215 N0R.12: 22 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: E.146, G.201, V.202, R.215, T.217, G.218, T.219, S.220 Ligands: ANP.10 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.146, B:G.201, B:R.215, B:R.215, A:R.314 pi-Cation interactions: B:R.215 Hydrophobic interactions: A:V.258, A:L.271, A:A.345 pi-Stacking: A:W.349

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 2 residues within 4Å: Chain A: E.146 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain B: E.146 Ligands: ANP.10 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: ANP.11 No protein-ligand interaction detected (PLIP)

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

EDO.6: 6 residues within 4Å: Chain A: L.30, T.69, I.71, R.94, F.95 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.7: 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: 7 residues within 4Å: Chain A: G.28, T.97, K.128, F.129 Chain B: K.256, D.260, Y.285 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.128, B:K.256 Water bridges: A:G.27 EDO.9: 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, B:E.237 Water bridges: A:K.286 EDO.15: 6 residues within 4Å: Chain B: L.30, T.69, I.71, R.94, F.95 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94 EDO.16: 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 EDO.17: 7 residues within 4Å: Chain A: K.256, D.260, Y.285 Chain B: G.28, T.97, K.128, F.129 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.128, A:K.256 Water bridges: B:G.27 EDO.18: 6 residues within 4Å: Chain A: L.227, S.231, C.236, E.237 Chain B: I.284, R.289 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.289, B:R.289, A:E.237, A:E.237 Water bridges: B:K.286

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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