SMTL ID : 5yib.1

Crystal Structure of KNI-10743 bound Plasmepsin II (PMII) from Plasmodium falciparum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x 8VC: (4R)-3-[(2S,3S)-3-[2-[4-[2-(dimethylamino)ethyl-methyl-amino]-2,6-dimethyl-phenoxy]ethanoylamino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-N-[(1S,2R)-2-oxidanyl-2,3-dihydro-1H-inden-1-yl]-1,3-thiazolidine-4-carboxamide(Non-covalent)

8VC.1: 25 residues within 4Å: Chain A: I.31, D.33, G.35, S.36, M.74, Y.76, V.77, S.78, F.110, I.122, D.129, L.130, S.131, I.132, D.213, G.215, T.216, S.217, T.220, I.289, L.291, F.293, I.299 Ligands: EDO.7, CPS.9 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.31, A:I.31, A:V.77, A:V.77, A:I.122, A:T.216, A:T.220, A:I.289, A:L.291, A:F.293, A:I.299 Hydrogen bonds: A:G.35, A:V.77, A:S.78, A:G.215, A:G.215, A:S.217

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.3: 4 residues within 4Å: Chain A: S.217, F.243, M.285, N.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.217, A:N.287 GOL.4: 3 residues within 4Å: Chain A: K.45, Y.65, K.67 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.45, A:K.67 Water bridges: A:S.59, A:S.59, A:Y.65, A:Y.65 GOL.5: 4 residues within 4Å: Chain A: N.232, L.233, D.234, V.235 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.232, A:D.234, A:D.234 Water bridges: A:L.230, A:V.235 GOL.6: 6 residues within 4Å: Chain A: T.195, D.197, K.207, T.259, S.260, E.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.197, A:T.259, A:E.261

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

EDO.7: 4 residues within 4Å: Chain A: G.35, Y.191, I.211 Ligands: 8VC.1 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain A: T.266, K.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.307 Water bridges: A:Y.308, A:Y.308

1 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.9: 7 residues within 4Å: Chain A: V.77, S.78, T.113, P.242, F.243, L.291 Ligands: 8VC.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.77, A:F.243, A:L.291 Hydrogen bonds: A:T.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mishra, V. et al., Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights. Febs J. (2018)

Release Date

2018-07-11

Peptides

Plasmepsin II: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Plasmepsin II

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