SMTL ID : 6x4k.1

PANK3 complex structure with compound PZ-2890

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x UOP: 4-(6-cyanopyridazin-3-yl)-N-[4-(propan-2-yl)phenyl]-3,4-dihydropyrazine-1(2H)-carboxamide(Non-covalent)

UOP.1: 20 residues within 4Å: Chain A: E.146, V.202, S.203, R.215, G.218, T.219 Chain B: V.258, I.261, 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 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.258, B:I.261, B:Y.266, B:L.271, B:A.277, B:A.345 Hydrogen bonds: B:V.276, B:R.314, A:R.215, A:R.215 pi-Stacking: B:W.349 pi-Cation interactions: A:R.215 UOP.7: 20 residues within 4Å: Chain A: V.258, I.261, 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, G.218, T.219 Ligands: ANP.8 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.258, A:I.261, A:Y.266, A:L.271, A:A.277, A:A.345 Hydrogen bonds: A:V.276, A:R.314, B:R.215, B:R.215 pi-Stacking: A:W.349 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: UOP.1, MG.3, EDO.4 24 PLIP interactions: 24 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:D.25, A:D.25, A:E.146, A:E.146, A:E.146, A:N.197, A:G.199, A:R.333 Salt bridges: A:K.32 pi-Stacking: A:F.239 ANP.8: 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: UOP.7, MG.9, EDO.10 24 PLIP interactions: 24 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:D.25, B:D.25, B:T.29, B:E.146, B:E.146, 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.3: 1 residues within 4Å: Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: ANP.8 No protein-ligand interaction detected (PLIP)

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

EDO.4: 7 residues within 4Å: Chain A: L.30, T.69, I.71, R.94, F.95, P.96 Ligands: ANP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.5: 6 residues within 4Å: Chain A: Y.262, D.265, Y.266, E.267, R.268 Chain B: Y.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.265, A:E.267, A:R.268 EDO.10: 7 residues within 4Å: Chain B: L.30, T.69, I.71, R.94, F.95, P.96 Ligands: ANP.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94 EDO.11: 6 residues within 4Å: Chain A: Y.127 Chain B: Y.262, 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 CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: L.141, H.142, K.143 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: L.141, H.142, K.143 Ligand excluded by PLIP

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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