SMTL ID : 7ue5.1

PANK3 complex structure with compound PZ-3741

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

2 x Y88: 6-[4-({4-[(2R)-1,1,1-trifluoropropan-2-yl]phenyl}acetyl)piperazin-1-yl]pyridazine-3-carbonitrile(Non-covalent)

Y88.1: 23 residues within 4Å: Chain A: E.146, V.202, S.203, 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: Y99.2, ANP.3 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.258, B:Y.266, B:L.271, B:A.345 Hydrogen bonds: B:R.314, A:R.215, A:R.215 pi-Stacking: B:W.349 pi-Cation interactions: A:R.215 Y88.5: 23 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, V.202, S.203, R.215, T.217, G.218, T.219 Ligands: Y99.6, ANP.7 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.258, A:Y.266, A:L.271, A:A.345 Hydrogen bonds: A:R.314, B:R.215, B:R.215 pi-Stacking: A:W.349 pi-Cation interactions: B:R.215

2 x Y99: 6-[4-({4-[(2S)-1,1,1-trifluoropropan-2-yl]phenyl}acetyl)piperazin-1-yl]pyridazine-3-carbonitrile(Non-covalent)

Y99.2: 23 residues within 4Å: Chain A: E.146, V.202, S.203, 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: Y88.1, ANP.3 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.258, B:I.261, B:L.271, B:A.345 Hydrogen bonds: B:R.314, A:R.215, A:R.215 pi-Stacking: B:W.349 pi-Cation interactions: A:R.215 Halogen bonds: A:R.215 Y99.6: 23 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, V.202, S.203, R.215, T.217, G.218, T.219 Ligands: Y88.5, ANP.7 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.258, A:I.261, A:L.271, A:A.345 Hydrogen bonds: A:R.314, B:R.215, B:R.215 pi-Stacking: A:W.349 pi-Cation interactions: B:R.215 Halogen bonds: B:R.215

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

ANP.3: 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: Y88.1, Y99.2, MG.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.28, A:T.29, A:L.30, 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:E.146, A:N.197, A:N.197, A:N.197, A:G.199, A:R.333 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: Y88.5, Y99.6, MG.8 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, B:L.30, 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:E.146, B:N.197, B:N.197, B:N.197, B:G.199, B:R.333 Salt bridges: B:K.32 pi-Stacking: B:F.239

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

MG.4: 1 residues within 4Å: Ligands: ANP.3 No protein-ligand interaction detected (PLIP) MG.8: 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., Development of Brain Penetrant Pyridazine Pantothenate Kinase Activators. J.Med.Chem. (2024)

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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