SMTL ID : 6x4l.1

PANK3 complex structure with compound PZ-3565

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x UOS: 1-[4-(5-chloropyrazin-2-yl)piperazin-1-yl]-2-[4-(propan-2-yl)phenyl]ethan-1-one(Non-covalent)

UOS.1: 19 residues within 4Å: Chain A: E.146, V.202, S.203, R.215, T.217, G.218, T.219 Chain B: I.261, Y.266, L.271, V.276, A.277, G.310, S.311, R.314, A.345, L.346, W.349 Ligands: ANP.2 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.215, A:R.215, B:R.314 pi-Cation interactions: A:R.215 Hydrophobic interactions: B:I.261, B:Y.266, B:L.271, B:A.277 pi-Stacking: B:W.349 UOS.7: 19 residues within 4Å: Chain A: I.261, Y.266, L.271, V.276, A.277, 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: ANP.8 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.261, A:Y.266, A:L.271, A:A.277 Hydrogen bonds: 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: 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: UOS.1, MG.3, EDO.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: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: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.8: 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: UOS.7, MG.9, EDO.10 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: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: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-covalent)

MG.3: 2 residues within 4Å: Chain A: K.32 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: K.32 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: I.284, R.289 Chain B: L.227, S.231, C.236, E.237 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.237, A:K.286, A:R.289, A:R.289 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: L.227, S.231, C.236, E.237 Chain B: I.284, R.289 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.237, A:E.237, B:K.286, B:R.289, B:R.289

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

Related Entries With Identical Sequence