SMTL ID : 8ez4.2 (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: 22 residues within 4Å: Chain A: K.290, D.295, K.302, M.308, M.312, F.314, D.315, D.375, E.377, T.402, L.403, T.404, G.405, A.406, L.408, Y.409, A.493, W.497, F.499 Ligands: CO3.6, ZN.7, ZN.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.314, A:L.408, A:Y.409, A:A.493 Hydrogen bonds: A:K.302, A:G.405 Water bridges: A:K.290, A:G.378, A:A.406 X10.10: 22 residues within 4Å: Chain B: K.290, D.295, K.302, M.308, L.311, F.314, D.315, D.375, E.377, L.403, T.404, G.405, A.406, L.408, Y.409, A.493, G.494, W.497, F.499 Ligands: CO3.13, ZN.15, ZN.16 12 PLIP interactions: 12 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:L.403, B:G.405 Water bridges: B:D.295, B:D.295, B:S.470, B:S.470 X10.18: 19 residues within 4Å: Chain C: K.290, D.295, K.302, M.308, F.314, D.375, E.377, T.402, L.403, T.404, G.405, A.406, L.408, Y.409, A.493, F.499 Ligands: CO3.23, ZN.24, ZN.25 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.314, C:L.408, C:Y.409 Hydrogen bonds: C:K.290, C:K.302, C:G.405 Water bridges: C:S.470 X10.27: 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: CO3.31, ZN.32, ZN.33 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.290, D:K.302, D:D.375, D:L.403, D:G.405 Water bridges: D:K.302, D:S.470 X10.35: 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 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.314, E:Y.409, E:A.493 Hydrogen bonds: E:K.302, E:G.405 Water bridges: E:D.375, E:A.406, E:S.470 X10.43: 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 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:F.314, F:L.408, F:Y.409, F:A.493 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:G.378, F:S.470, F:S.470

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

SO4.2: 6 residues within 4Å: Chain A: E.41, G.42, K.134, L.135, S.136 Chain D: K.80 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:G.42, A:S.136, A:K.137 Water bridges: D:K.80, D:K.80 Salt bridges: D:K.80 SO4.3: 5 residues within 4Å: Chain A: I.17, E.18, Y.19, N.20 Ligands: 1PE.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.18, A:Y.19, A:N.20, A:N.20 SO4.11: 6 residues within 4Å: Chain A: S.351, K.352 Chain B: S.351, K.352 Chain C: S.351, K.352 8 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: C:S.351, C:K.352, A:K.352, B:S.351, B:K.352 Salt bridges: A:K.352, B:K.352 Water bridges: B:K.352 SO4.19: 5 residues within 4Å: Chain C: I.17, E.18, Y.19, N.20 Ligands: 1PE.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.19, C:N.20, C:N.20, C:N.20 SO4.28: 5 residues within 4Å: Chain D: I.17, E.18, Y.19, N.20 Ligands: 1PE.30 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.19, D:N.20, D:N.20, D:N.20 Water bridges: D:I.17 SO4.44: 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: 1 interactions with chain D, 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: D:K.352, F:K.352, E:K.352 Water bridges: F:K.352 Salt bridges: F:K.352, E:K.352

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

1PE.4: 7 residues within 4Å: Chain A: Y.19, N.20, H.24, F.205, K.236, L.237, Y.327 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.236 Water bridges: A:Y.327, A:Y.327, A:Y.327 1PE.5: 4 residues within 4Å: Chain A: Y.19, E.232, K.236 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.232, A:K.236 1PE.12: 5 residues within 4Å: Chain B: Y.19, H.24, K.236, Y.327 Ligands: 2PE.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.24, B:K.236 Water bridges: B:Y.327, B:Y.327 1PE.20: 6 residues within 4Å: Chain C: Y.19, E.232, Q.235, K.236 Ligands: SO4.19, 1PE.21 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.236 Hydrogen bonds: C:K.236 1PE.21: 7 residues within 4Å: Chain C: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligands: 1PE.20 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.20 Water bridges: C:Y.327, C:Y.327 1PE.22: 6 residues within 4Å: Chain C: Y.31, G.35, G.36, N.38, N.65, Y.186 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.38, C:N.65, C:Y.186 1PE.29: 5 residues within 4Å: Chain D: Y.19, H.24, F.205, K.236, Y.327 No protein-ligand interaction detected (PLIP) 1PE.30: 6 residues within 4Å: Chain D: Y.19, N.20, E.232, Q.235, K.236 Ligands: SO4.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.236 1PE.36: 6 residues within 4Å: Chain E: Y.19, N.20, H.24, F.205, K.236, Y.327 2 PLIP interactions: 2 interactions with chain E Water bridges: E:T.331, E:T.331 1PE.37: 3 residues within 4Å: Chain E: Y.19, E.232, K.236 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.236 Water bridges: E:K.236 1PE.38: 6 residues within 4Å: Chain E: N.365, K.367, D.459, E.480, Q.483 Chain F: S.170 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.367, E:R.450, E:E.480 1PE.45: 6 residues within 4Å: Chain F: Y.19, H.24, F.205, K.236, Y.327 Ligands: 1PE.46 No protein-ligand interaction detected (PLIP) 1PE.46: 4 residues within 4Å: Chain F: Y.19, E.232, K.236 Ligands: 1PE.45 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.235, F:K.236 1PE.47: 7 residues within 4Å: Chain D: S.170 Chain F: N.365, K.367, R.450, D.459, E.480, Q.483 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:K.367, F:R.450, F:E.480, F:E.480, F:E.480, F:Q.483, D:S.170

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

CO3.6: 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, A:R.379, A:R.379 CO3.13: 7 residues within 4Å: Chain B: D.375, A.376, E.377, G.378, R.379, L.403 Ligands: X10.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.376, B:G.378, B:R.379, B:R.379, B:R.379 CO3.23: 8 residues within 4Å: Chain C: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: X10.18, ZN.24 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.376, C:G.378, C:R.379, C:L.403 CO3.31: 7 residues within 4Å: Chain D: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: X10.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.379, D:R.379, D:L.403 CO3.39: 7 residues within 4Å: Chain E: A.376, E.377, G.378, R.379, L.403, T.404 Ligands: X10.35 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.379, E:R.379, E:L.403 Water bridges: E:E.377 CO3.48: 6 residues within 4Å: Chain F: A.376, E.377, G.378, R.379, L.403 Ligands: X10.43 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.379 Water bridges: F:G.378

12 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: K.290, D.295, D.315, E.377 Ligands: X10.1, ZN.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.295, A:D.315, A:E.377, H2O.7 ZN.8: 6 residues within 4Å: Chain A: D.295, K.302, D.375, E.377 Ligands: X10.1, ZN.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.295, A:D.375, A:D.375, A:E.377 ZN.15: 6 residues within 4Å: Chain B: K.290, D.295, D.315, E.377 Ligands: X10.10, ZN.16 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.295, B:D.315, B:E.377, H2O.22 ZN.16: 6 residues within 4Å: Chain B: D.295, K.302, D.375, E.377 Ligands: X10.10, 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.24: 7 residues within 4Å: Chain C: K.290, D.295, D.315, E.377 Ligands: X10.18, CO3.23, ZN.25 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.295, C:D.315, C:E.377 ZN.25: 6 residues within 4Å: Chain C: D.295, K.302, D.375, E.377 Ligands: X10.18, ZN.24 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.295, C:D.375, C:D.375, C:E.377 ZN.32: 6 residues within 4Å: Chain D: K.290, D.295, D.315, E.377 Ligands: X10.27, ZN.33 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.295, D:D.315, D:E.377, H2O.52 ZN.33: 6 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: X10.27, ZN.32 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.295, D:D.375, D:D.375, D:E.377 ZN.40: 6 residues within 4Å: Chain E: K.290, D.295, D.315, E.377 Ligands: X10.35, ZN.41 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.295, E:D.315, E:E.377, H2O.62, H2O.74 ZN.41: 6 residues within 4Å: Chain E: D.295, K.302, D.375, E.377 Ligands: X10.35, 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: 6 residues within 4Å: Chain F: K.290, D.295, D.315, E.377 Ligands: X10.43, 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.86 ZN.50: 6 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: X10.43, ZN.49 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.295, F:D.375, F:D.375, F:E.377

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

NA.9: 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:A.216 NA.17: 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:A.216 NA.26: 6 residues within 4Å: Chain C: L.213, I.214, A.216, C.221, K.313, M.316 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.214 NA.34: 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:L.213 NA.42: 6 residues within 4Å: Chain E: L.213, I.214, A.216, C.221, K.313, M.316 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.216

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.14: 5 residues within 4Å: Chain B: Y.19, E.232, Q.235, K.236 Ligands: 1PE.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.236 Water bridges: B:Y.19

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
G

B
H

C
I

D
J

E
K

F
L

M17 leucyl aminopeptidase

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