SMTL ID : 6c4g.1

Plasmepsin V from Plasmodium vivax bound to a transition state mimetic (WEHI-601)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.323, P.329, L.330, V.331, F.333 No protein-ligand interaction detected (PLIP)

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

NAG.2: 1 residues within 4Å: Chain A: N.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.248

1 x EQG: benzyl [(6S,7S,10S,13S,18Z)-18-amino-10-cyclohexyl-6-hydroxy-18-imino-7-(2-methylpropyl)-4,9,12-trioxo-1-phenyl-16-oxa-3,8,11,17-tetraazaoctadecan-13-yl]carbamate(Non-covalent)

EQG.3: 27 residues within 4Å: Chain A: A.28, Y.29, I.46, D.48, G.50, S.51, Q.105, S.106, Y.107, C.108, E.109, L.147, F.148, Q.151, V.156, Y.256, L.279, D.281, G.283, S.284, T.285, F.286, H.288, V.402, K.405, I.407 Ligands: EDO.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.107, A:Y.107, A:E.109, A:F.148, A:V.402, A:I.407 Hydrogen bonds: A:G.50, A:C.108, A:E.109, A:E.109, A:Q.151, A:Q.151, A:D.281, A:G.283, A:T.285, A:T.285, A:T.285 Water bridges: A:F.286 Salt bridges: A:E.109 pi-Cation interactions: A:F.148

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

EDO.4: 3 residues within 4Å: Chain A: Y.201, W.246, R.426 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.426, A:R.426 EDO.5: 6 residues within 4Å: Chain A: S.51, S.52, Q.105, S.160, Y.254 Ligands: EQG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.52, A:Q.105, A:Q.105, A:S.160, A:S.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, W. et al., Enhanced antimalarial activity of plasmepsin V inhibitors by modification of the P2position of PEXEL peptidomimetics. Eur J Med Chem (2018)

Release Date

2018-06-13

Peptides

Aspartic protease PM5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aspartic protease PM5

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