SMTL ID : 7ue3.1

PANK3 complex structure with compound PZ-3804

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

2 x ND6: 6-[4-({4-[(2R)-1-hydroxypropan-2-yl]phenyl}acetyl)piperazin-1-yl]pyridazine-3-carbonitrile(Non-covalent)

ND6.1: 23 residues within 4Å: Chain A: E.146, G.201, V.202, S.203, R.215, T.217, G.218, T.219, S.220 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 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:G.201, A:R.215, A:R.215, B:R.314 pi-Cation interactions: A:R.215 Hydrophobic interactions: B:V.258, B:Y.266, B:L.271, B:A.277, B:A.345 pi-Stacking: B:W.349 ND6.13: 23 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, G.201, V.202, S.203, R.215, T.217, G.218, T.219, S.220 Ligands: ANP.14 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.258, A:Y.266, A:L.271, A:A.277, A:A.345 Hydrogen bonds: A:R.314, B:G.201, B:R.215, B:R.215 pi-Stacking: A:W.349 pi-Cation interactions: B:R.215

4 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: ND6.1, MG.4, EDO.6 26 PLIP interactions: 26 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:K.32, A:R.94, A:E.146, A:E.146, A:N.197, A:N.197, A:N.197, A:G.199 Salt bridges: A:K.32 pi-Stacking: A:F.239 ANP.3: 8 residues within 4Å: Chain A: D.80, L.81, T.82, S.159, V.160, S.161 Ligands: MG.5, EDO.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.82, A:T.82, A:S.161 Water bridges: A:T.82 ANP.14: 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: ND6.13, MG.16, EDO.18 28 PLIP interactions: 28 interactions with chain B Hydrogen bonds: B:G.28, B:T.29, B:L.30, B:L.30, B:K.32, B:E.146, 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:K.32, B:R.94, B:E.146, B:E.146, B:N.197, B:N.197, B:N.197, B:G.199 Salt bridges: B:K.32 pi-Stacking: B:F.239 ANP.15: 8 residues within 4Å: Chain B: D.80, L.81, T.82, S.159, V.160, S.161 Ligands: MG.17, EDO.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.82, B:T.82, B:S.161 Water bridges: B:Y.156

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

MG.4: 1 residues within 4Å: Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: ANP.3 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: ANP.14 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Ligands: ANP.15 No protein-ligand interaction detected (PLIP)

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

EDO.6: 6 residues within 4Å: Chain A: L.30, T.69, I.71, R.94, F.95 Ligands: ANP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.94 EDO.7: 5 residues within 4Å: Chain A: 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.8: 6 residues within 4Å: Chain A: G.28, T.97, K.128, F.129 Chain B: D.260, Y.285 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.285, A:K.128 EDO.9: 7 residues within 4Å: Chain A: I.284, R.289 Chain B: L.227, S.231, C.236, E.237, S.238 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:E.237, A:K.286 Hydrogen bonds: A:R.289, A:R.289 EDO.10: 7 residues within 4Å: Chain A: L.78, K.79, V.160, S.161, F.162, N.163 Ligands: ANP.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.79, A:S.161, A:N.163 EDO.11: 8 residues within 4Å: Chain A: F.327, V.328, G.329, L.332, M.339, F.358, L.359, E.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.327, A:L.359, A:E.362 EDO.12: 6 residues within 4Å: Chain A: L.243, S.247, V.334, N.335, T.336, L.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.335, A:T.336, A:L.337 EDO.18: 6 residues within 4Å: Chain B: L.30, T.69, I.71, R.94, F.95 Ligands: ANP.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.94 EDO.19: 5 residues within 4Å: Chain A: Y.127 Chain B: 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 EDO.20: 6 residues within 4Å: Chain A: D.260, Y.285 Chain B: G.28, T.97, K.128, F.129 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.285 Hydrogen bonds: B:K.128 EDO.21: 7 residues within 4Å: Chain A: L.227, S.231, C.236, E.237, S.238 Chain B: I.284, R.289 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:E.237, B:K.286 Hydrogen bonds: B:R.289, B:R.289 EDO.22: 7 residues within 4Å: Chain B: L.78, K.79, V.160, S.161, F.162, N.163 Ligands: ANP.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.79, B:S.161, B:N.163 EDO.23: 8 residues within 4Å: Chain B: F.327, V.328, G.329, L.332, M.339, F.358, L.359, E.362 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.327, B:L.359, B:E.362 EDO.24: 6 residues within 4Å: Chain B: L.243, S.247, V.334, N.335, T.336, L.337 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.335, B:T.336, B:L.337

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

Related Entries With Identical Sequence