SMTL ID : 7tbc.1

Crystal structure of Plasmepsin X from Plasmodium falciparum in complex with WM382

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: I.143, T.249, S.250, M.315 Ligands: EDO.9, I0L.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.249, A:S.250, A:S.250 EDO.4: 3 residues within 4Å: Chain A: G.44, T.45, P.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.45 EDO.5: 3 residues within 4Å: Chain A: S.72, K.75, D.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.75 EDO.6: 2 residues within 4Å: Chain A: K.75, V.76 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain A: N.82, S.84 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain A: H.97, S.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.106, A:S.106 EDO.9: 4 residues within 4Å: Chain A: S.102, D.141, I.143 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.141 EDO.10: 3 residues within 4Å: Chain A: Y.186, S.204, S.360 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.186, A:S.360 EDO.11: 2 residues within 4Å: Chain A: Y.220 Ligands: I0L.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.220, A:Y.220 EDO.12: 4 residues within 4Å: Chain A: I.235, D.238, Q.258, T.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.238, A:Q.258, A:T.261 EDO.13: 3 residues within 4Å: Chain A: P.177, N.178, V.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.180 EDO.14: 3 residues within 4Å: Chain A: D.170, R.344, G.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.345 EDO.15: 2 residues within 4Å: Chain A: P.158, L.161 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain A: L.293, I.294 No protein-ligand interaction detected (PLIP) EDO.17: 2 residues within 4Å: Chain A: E.71, K.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.71

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: N.123, N.165 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.165

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 4 residues within 4Å: Chain A: I.24, Q.182, G.200, I.201 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.182, A:I.201

1 x I0L: (4R)-4-[(2E)-4,4-diethyl-2-imino-6-oxo-1,3-diazinan-1-yl]-N-[(4S)-2,2-dimethyl-3,4-dihydro-2H-1-benzopyran-4-yl]-3,4-dihydro-2H-1-benzopyran-6-carboxamide(Non-covalent)

I0L.18: 19 residues within 4Å: Chain A: S.35, Q.36, I.53, D.55, G.57, S.58, F.100, S.102, F.144, I.147, F.149, I.152, D.246, G.248, S.250, I.317, L.328 Ligands: EDO.1, EDO.11 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.36, A:I.53, A:F.100, A:F.100, A:F.144, A:I.147, A:F.149, A:I.152, A:L.328 Hydrogen bonds: A:S.58, A:S.102, A:G.248 Salt bridges: A:D.55, A:D.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hodder, A.N. et al., Basis for drug selectivity of plasmepsin IX and X inhibition in Plasmodium falciparum and vivax. Structure (2022)

Release Date

2022-05-04

Peptides

Plasmepsin 10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Plasmepsin 10

Related Entries With Identical Sequence