SMTL ID : 7ueu.1

PANK3 complex structure with compound PZ-4215

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x YX5: N-(4-{2-[4-(6-cyanopyridazin-3-yl)piperazin-1-yl]-2-oxoethyl}phenyl)ethanesulfonamide(Non-covalent)

YX5.1: 22 residues within 4Å: Chain A: E.146, G.201, V.202, S.203, R.215, G.218, T.219, S.220 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 11 PLIP interactions: 6 interactions with chain B, 5 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 Water bridges: A:G.28, A:G.201 pi-Cation interactions: A:R.215 YX5.5: 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, S.203, R.215, G.218, T.219, S.220 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.215, B:R.215, A:R.314 Water bridges: B:G.28, B:G.201 pi-Cation interactions: B:R.215 Hydrophobic interactions: A:V.258, A:L.271, A:A.277, A:A.345 pi-Stacking: A:W.349

2 x AN2: AMP PHOSPHORAMIDATE(Non-covalent)

AN2.2: 18 residues within 4Å: Chain A: G.27, G.28, T.29, L.30, K.32, I.198, G.199, S.200, G.223, G.224, F.239, E.240, G.329, N.330, F.331, R.333 Ligands: MG.3, EDO.4 19 PLIP interactions: 19 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.223, A:E.240, A:N.330, A:N.330, A:F.331, A:R.333 Water bridges: A:S.200, A:G.201, A:R.333, A:G.363 Salt bridges: A:K.32 pi-Stacking: A:F.239 AN2.6: 18 residues within 4Å: Chain B: G.27, G.28, T.29, L.30, K.32, I.198, G.199, S.200, G.223, G.224, F.239, E.240, G.329, N.330, F.331, R.333 Ligands: MG.7, EDO.8 20 PLIP interactions: 20 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.223, B:E.240, B:N.330, B:N.330, B:F.331, B:R.333 Water bridges: B:T.29, B:S.200, B:G.201, B:R.333, B:G.363 Salt bridges: B:K.32 pi-Stacking: B:F.239

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.146 Ligands: AN2.2 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: E.146 Ligands: AN2.6 No protein-ligand interaction detected (PLIP)

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

EDO.4: 6 residues within 4Å: Chain A: L.30, T.69, I.71, R.94, F.95 Ligands: AN2.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.8: 6 residues within 4Å: Chain B: L.30, T.69, I.71, R.94, F.95 Ligands: AN2.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94

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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