SMTL ID : 6sbq.1

The crystal structure of PfA-M1 in complex with 7-amino-4-phenyl-5,7,8,9-tetrahydrobenzocyclohepten-6-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.335, H.339, E.358, Y.419 Ligands: 7ML.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.335, A:H.339, A:E.358, A:E.358

1 x 7ML: [(7~{S})-6,6-bis(oxidanyl)-4-phenyl-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium(Non-covalent)

7ML.2: 18 residues within 4Å: Chain A: E.158, V.298, G.299, A.300, M.301, E.302, R.328, T.331, V.332, H.335, E.336, H.339, K.357, E.358, V.362, Y.414, Y.419 Ligands: ZN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.298, A:V.298, A:V.298, A:V.332, A:Y.414, A:Y.414, A:Y.419 Hydrogen bonds: A:E.158, A:E.336, A:K.357, A:Y.419 pi-Stacking: A:H.335, A:Y.419

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: Y.692, S.742, L.743, K.746, A.747 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.743 PEG.8: 12 residues within 4Å: Chain A: V.664, Y.692, K.693, I.695, G.696, L.699, N.700, Y.703, L.743, L.744, A.747 Ligands: PEG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.664, A:G.696, A:N.700, A:Y.703, A:L.743

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 7 residues within 4Å: Chain A: V.191, L.193, K.198, H.233, Y.250, F.252, R.287 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.250 Water bridges: A:L.192, A:L.192, A:K.198, A:K.198, A:K.198, A:K.198, A:K.198, A:H.233, A:R.287 Salt bridges: A:K.198, A:K.198, A:H.233, A:R.287 MLI.5: 3 residues within 4Å: Chain A: S.119, K.120, K.124 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.119, A:K.124, A:K.124 Salt bridges: A:K.124

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: E.796, N.831 Ligands: NA.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.796, A:E.796 Water bridges: A:K.150, A:S.829, A:D.834 NA.7: 1 residues within 4Å: Ligands: NA.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.829, A:S.829

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salomon, E. et al., Aminobenzosuberone derivatives as PfA-M1 inhibitors: Molecular recognition and antiplasmodial evaluation. Bioorg.Chem. (2020)

Release Date

2020-03-25

Peptides

M1-family alanyl aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1-family alanyl aminopeptidase

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