SMTL ID : 6x4j.1

PANK3 complex structure with compound PZ-2863

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.25, K.32 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: D.25, K.32 Ligands: ANP.6 No protein-ligand interaction detected (PLIP)

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: MG.1, UOM.3, EDO.4 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:F.331, A:R.333 Water bridges: A:K.32, A:E.146, A:N.197, A:N.197, A:N.197, A:G.199, A:G.199 Salt bridges: A:K.32 pi-Stacking: A:F.239 ANP.6: 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: MG.5, UOM.7, EDO.8 25 PLIP interactions: 25 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:F.331, B:R.333 Water bridges: B:T.29, B:K.32, B:E.146, B:N.197, B:N.197, B:N.197, B:G.199, B:G.199 Salt bridges: B:K.32 pi-Stacking: B:F.239

2 x UOM: 6-(4-{[4-(propan-2-yl)phenyl]acetyl}piperazin-1-yl)pyridine-3-carbonitrile(Non-covalent)

UOM.3: 18 residues within 4Å: Chain A: E.146, V.202, S.203, R.215, G.218, T.219, S.220 Chain B: I.261, L.271, V.276, A.277, N.307, G.310, S.311, A.345, L.346, W.349 Ligands: ANP.2 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.261, B:L.271, B:A.345 pi-Stacking: B:W.349 Hydrogen bonds: A:R.215, A:R.215 Water bridges: A:T.217 pi-Cation interactions: A:R.215 UOM.7: 18 residues within 4Å: Chain A: I.261, L.271, V.276, A.277, N.307, G.310, S.311, A.345, L.346, W.349 Chain B: E.146, V.202, S.203, R.215, G.218, T.219, S.220 Ligands: ANP.6 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.261, A:L.271, A:A.345 pi-Stacking: A:W.349 Hydrogen bonds: B:R.215, B:R.215 pi-Cation interactions: B:R.215

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, P.96 Ligands: ANP.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, P.96 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, L.K. et al., LipE guided discovery of isopropylphenyl pyridazines as pantothenate kinase modulators. Bioorg.Med.Chem. (2021)

Release Date

2021-11-24

Peptides

Pantothenate kinase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase 3

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