SMTL ID : 8tyg.1

Plasmodium vivax PMV-WM08 inhibitor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 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: 1 residues within 4Å: Chain A: N.248 No protein-ligand interaction detected (PLIP)

1 x SKC: (2E,4aR,7aS)-6-[3-(4-chlorophenyl)pyridin-2-yl]-7a-(2,5-difluorophenyl)-2-imino-3-methyloctahydro-4H-pyrrolo[3,4-d]pyrimidin-4-one(Non-covalent)

SKC.2: 20 residues within 4Å: Chain A: Y.29, I.46, D.48, G.50, S.51, S.55, Y.103, Q.105, S.106, Y.107, I.113, H.141, L.147, F.148, Q.151, V.156, D.281, G.283, S.284, I.407 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.46, A:Q.105, A:Q.105, A:L.147, A:V.156 Water bridges: A:C.108, A:D.281 Salt bridges: A:D.48, A:D.281

1 x TEW: 6-tungstotellurate(VI)(Non-covalent)

TEW.3: 5 residues within 4Å: Chain A: K.163, R.251, K.252, Y.253, Y.254 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.251, A:R.251, A:K.252, A:Y.253, A:Y.254

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

NAG.4: 4 residues within 4Å: Chain A: N.323, P.329, L.330, F.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.330, A:V.331 NAG.5: 3 residues within 4Å: Chain A: A.59, G.60, N.75 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.59 Hydrogen bonds: A:N.75 Water bridges: A:N.75

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 5 residues within 4Å: Chain A: V.351, K.390, E.391, S.392, F.393 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.391, A:S.392, A:F.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hodder, A.N. et al., Structure-activity analysis of imino-pyrimidinone-fused pyrrolidines aids the development of dual plasmepsin V and plasmepsin X inhibitors. Febs J. (2025)

Release Date

2024-08-28

Peptides

Plasmepsin V: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Plasmepsin V

Related Entries With Identical Sequence