SMTL ID : 8ez4.1 (1 other biounit)

Plasmodium falciparum M17 in complex with inhibitor 9aa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-hexamer

Ligands

6 x X10: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-N~2~-phenylglycinamide(Non-covalent)

X10.1: 19 residues within 4Å: Chain A: K.290, D.295, K.302, M.308, F.314, D.315, D.375, E.377, L.403, T.404, G.405, A.406, L.408, Y.409, A.493, F.499 Ligands: CO3.8, ZN.9, ZN.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.314, A:L.408, A:Y.409, A:A.493 Hydrogen bonds: A:K.290, A:K.302, A:G.405 Water bridges: A:K.302, A:D.375, A:A.406, A:S.470, A:S.470 X10.12: 18 residues within 4Å: Chain B: K.290, D.295, K.302, M.308, F.314, D.375, E.377, L.403, T.404, G.405, A.406, L.408, Y.409, A.493, F.499 Ligands: CO3.13, ZN.14, ZN.15 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.314, B:L.408, B:Y.409, B:A.493 Hydrogen bonds: B:K.290, B:K.302, B:G.405, B:A.406 Water bridges: B:K.302, B:D.375, B:A.376 X10.17: 19 residues within 4Å: Chain C: K.290, D.295, K.302, M.308, F.314, D.315, D.375, E.377, T.402, L.403, T.404, G.405, L.408, Y.409, A.493, F.499 Ligands: CO3.22, ZN.23, ZN.24 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.314, C:Y.409, C:A.493 Hydrogen bonds: C:K.290, C:K.302, C:D.375, C:L.403, C:G.405 Water bridges: C:K.302, C:A.406, C:S.470 X10.25: 20 residues within 4Å: Chain D: K.290, D.295, K.302, M.308, F.314, D.315, D.375, E.377, T.402, L.403, T.404, G.405, A.406, L.408, Y.409, A.493, F.499 Ligands: CO3.29, ZN.31, ZN.32 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.314, D:L.408, D:Y.409, D:A.493 Hydrogen bonds: D:K.302, D:L.403, D:G.405 Water bridges: D:K.302, D:G.378, D:A.406, D:A.406 X10.34: 19 residues within 4Å: Chain E: K.290, D.295, K.302, M.308, F.314, D.315, D.375, E.377, L.403, T.404, G.405, A.406, L.408, Y.409, A.493, F.499 Ligands: CO3.39, ZN.40, ZN.41 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:F.314, E:L.408, E:Y.409, E:A.493 Hydrogen bonds: E:K.290, E:K.302, E:G.405 Water bridges: E:D.375, E:S.470 X10.42: 19 residues within 4Å: Chain F: K.290, D.295, K.302, M.308, F.314, D.315, D.375, E.377, L.403, T.404, G.405, A.406, L.408, Y.409, A.493, F.499 Ligands: CO3.48, ZN.49, ZN.50 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:F.314, F:L.408, F:Y.409 Hydrogen bonds: F:K.290, F:K.302, F:D.375, F:L.403, F:G.405 Water bridges: F:D.295, F:D.295, F:K.302, F:D.375, F:S.470

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: S.351, K.352 Chain B: S.351, K.352 Chain C: S.351, K.352 9 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:S.351, C:K.352, B:S.351, B:K.352, A:K.352 Water bridges: C:K.352 Salt bridges: C:K.352, B:K.352, A:K.352 SO4.3: 5 residues within 4Å: Chain A: E.41, G.42, L.135, S.136 Chain D: K.80 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.42, A:S.136 Salt bridges: D:K.80 SO4.4: 5 residues within 4Å: Chain A: I.17, E.18, Y.19, N.20 Ligands: 1PE.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.19, A:N.20, A:N.20 SO4.18: 4 residues within 4Å: Chain C: E.18, Y.19, N.20 Ligands: 1PE.20 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.19, C:N.20, C:N.20 SO4.30: 6 residues within 4Å: Chain D: S.351, K.352 Chain E: S.351, K.352 Chain F: S.351, K.352 6 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: D:K.352, E:K.352, F:K.352 Water bridges: D:K.352 Salt bridges: D:K.352, F:K.352 SO4.35: 5 residues within 4Å: Chain E: I.17, E.18, Y.19, N.20 Ligands: 1PE.38 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:I.17, E:Y.19, E:N.20, E:N.20 SO4.43: 5 residues within 4Å: Chain F: I.17, E.18, Y.19, N.20 Ligands: 1PE.47 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.19, F:N.20

16 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 5 residues within 4Å: Chain A: Y.19, N.20, H.24, K.236, Y.327 Ligand excluded by PLIP 1PE.6: 5 residues within 4Å: Chain A: Y.31, G.36, N.38, E.40, Y.186 Ligand excluded by PLIP 1PE.7: 6 residues within 4Å: Chain A: Y.19, N.20, E.232, Q.235, K.236 Ligands: SO4.4 Ligand excluded by PLIP 1PE.19: 5 residues within 4Å: Chain C: Y.19, N.20, H.24, F.205, Y.327 Ligand excluded by PLIP 1PE.20: 5 residues within 4Å: Chain C: Y.19, E.232, Q.235, K.236 Ligands: SO4.18 Ligand excluded by PLIP 1PE.21: 6 residues within 4Å: Chain C: Y.31, G.35, G.36, N.38, N.65, Y.186 Ligand excluded by PLIP 1PE.26: 6 residues within 4Å: Chain D: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligand excluded by PLIP 1PE.27: 4 residues within 4Å: Chain D: Y.19, E.232, Q.235, K.236 Ligand excluded by PLIP 1PE.28: 4 residues within 4Å: Chain D: N.365, K.367, D.459 Chain E: S.170 Ligand excluded by PLIP 1PE.36: 6 residues within 4Å: Chain E: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligand excluded by PLIP 1PE.37: 7 residues within 4Å: Chain E: N.365, K.367, R.450, D.459, E.480, Q.483 Chain F: S.170 Ligand excluded by PLIP 1PE.38: 5 residues within 4Å: Chain E: Y.19, E.232, Q.235, K.236 Ligands: SO4.35 Ligand excluded by PLIP 1PE.44: 7 residues within 4Å: Chain D: S.170 Chain F: N.365, K.367, R.450, D.459, E.480, Q.483 Ligand excluded by PLIP 1PE.45: 6 residues within 4Å: Chain F: Y.19, H.24, F.205, K.236, L.237, Y.327 Ligand excluded by PLIP 1PE.46: 3 residues within 4Å: Chain F: H.24, E.198, R.201 Ligand excluded by PLIP 1PE.47: 5 residues within 4Å: Chain F: Y.19, E.232, Q.235, K.236 Ligands: SO4.43 Ligand excluded by PLIP

6 x CO3: CARBONATE ION(Non-functional Binders)

CO3.8: 6 residues within 4Å: Chain A: A.376, E.377, G.378, R.379, L.403 Ligands: X10.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.378, A:R.379 Water bridges: A:D.375, A:A.376 CO3.13: 7 residues within 4Å: Chain B: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: X10.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.378, B:R.379, B:R.379, B:R.379 CO3.22: 7 residues within 4Å: Chain C: D.375, A.376, E.377, G.378, R.379, L.403 Ligands: X10.17 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.376, C:G.378, C:R.379, C:L.403 CO3.29: 8 residues within 4Å: Chain D: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: X10.25 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.376, D:G.378, D:R.379, D:R.379, D:R.379 CO3.39: 9 residues within 4Å: Chain E: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: X10.34, ZN.40 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.379, E:R.379, E:L.403 CO3.48: 8 residues within 4Å: Chain F: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: X10.42, ZN.49 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.379, F:R.379, F:L.403

12 x ZN: ZINC ION(Non-covalent)

ZN.9: 6 residues within 4Å: Chain A: K.290, D.295, D.315, E.377 Ligands: X10.1, ZN.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.295, A:D.315, A:E.377, H2O.12 ZN.10: 6 residues within 4Å: Chain A: D.295, K.302, D.375, E.377 Ligands: X10.1, ZN.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.295, A:D.375, A:D.375, A:E.377 ZN.14: 6 residues within 4Å: Chain B: D.295, K.302, D.375, E.377 Ligands: X10.12, ZN.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.295, B:D.375, B:D.375, B:E.377 ZN.15: 6 residues within 4Å: Chain B: K.290, D.295, D.315, E.377 Ligands: X10.12, ZN.14 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.295, B:D.315, B:E.377, H2O.27 ZN.23: 6 residues within 4Å: Chain C: K.290, D.295, D.315, E.377 Ligands: X10.17, ZN.24 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.295, C:D.315, C:E.377, H2O.36 ZN.24: 6 residues within 4Å: Chain C: D.295, K.302, D.375, E.377 Ligands: X10.17, ZN.23 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.295, C:D.375, C:D.375, C:E.377 ZN.31: 6 residues within 4Å: Chain D: K.290, D.295, D.315, E.377 Ligands: X10.25, ZN.32 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.295, D:D.315, D:E.377, H2O.46 ZN.32: 6 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: X10.25, ZN.31 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.295, D:D.375, D:D.375, D:E.377 ZN.40: 7 residues within 4Å: Chain E: K.290, D.295, D.315, E.377 Ligands: X10.34, CO3.39, ZN.41 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.295, E:D.315, E:E.377, H2O.71 ZN.41: 6 residues within 4Å: Chain E: D.295, K.302, D.375, E.377 Ligands: X10.34, ZN.40 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.295, E:D.375, E:D.375, E:E.377 ZN.49: 7 residues within 4Å: Chain F: K.290, D.295, D.315, E.377 Ligands: X10.42, CO3.48, ZN.50 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.295, F:D.315, F:E.377, H2O.84 ZN.50: 6 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: X10.42, ZN.49 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.295, F:D.375, F:D.375, F:E.377

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

NA.11: 6 residues within 4Å: Chain A: L.213, I.214, A.216, C.221, K.313, M.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.313 NA.16: 6 residues within 4Å: Chain B: L.213, I.214, A.216, C.221, K.313, M.316 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.214 NA.33: 6 residues within 4Å: Chain D: L.213, I.214, A.216, C.221, K.313, M.316 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.313 NA.51: 6 residues within 4Å: Chain F: L.213, I.214, A.216, C.221, K.313, M.316 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:I.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calic, P.P.S. et al., Structure-based development of potent Plasmodium falciparum M1 and M17 aminopeptidase selective and dual inhibitors via S1'-region optimisation. Eur.J.Med.Chem. (2022)

Release Date

2023-01-18

Peptides

M17 leucyl aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

M17 leucyl aminopeptidase

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