SMTL ID : 6eee.1 (1 other biounit)

X-ray crystal structure of Pf-M17 in complex with inhibitor (6k) and regulatory zinc ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

6 x J4V: (1R,2r,3S,5R,7R)-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]tricyclo[3.3.1.1~3,7~]decane-2-carboxamide(Non-covalent)

J4V.1: 23 residues within 4Å: Chain A: K.290, D.295, K.302, G.306, M.308, L.311, M.312, F.314, D.315, N.373, D.375, A.376, E.377, T.402, L.403, T.404, G.405, L.408, S.470, A.493, F.499 Ligands: CO3.2, ZN.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.314, A:A.376, A:L.408 Hydrogen bonds: A:K.290, A:K.302, A:D.375, A:D.375, A:L.403, A:G.405 Water bridges: A:S.470 pi-Cation interactions: A:K.302 Halogen bonds: A:G.306 J4V.11: 21 residues within 4Å: Chain B: K.290, D.295, K.302, G.306, M.308, L.311, D.315, N.373, D.375, A.376, E.377, R.379, T.402, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.12, ZN.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.376 Hydrogen bonds: B:K.290, B:K.302, B:D.375, B:E.377, B:L.403, B:G.405 Water bridges: B:S.470 Halogen bonds: B:G.306 J4V.19: 22 residues within 4Å: Chain C: K.290, D.295, K.302, G.306, M.308, M.312, F.314, D.315, N.373, D.375, A.376, E.377, R.379, L.403, T.404, G.405, L.408, S.470, A.493, F.499 Ligands: CO3.20, ZN.21 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.314, C:A.376 Hydrogen bonds: C:K.290, C:K.302, C:D.375, C:L.403, C:G.405 Water bridges: C:A.406 J4V.27: 20 residues within 4Å: Chain D: K.290, D.295, K.302, G.306, M.308, M.312, D.315, N.373, D.375, A.376, E.377, R.379, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.28, ZN.29 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:A.376 Hydrogen bonds: D:K.290, D:K.302, D:D.375, D:L.403, D:G.405 J4V.35: 23 residues within 4Å: Chain E: K.290, D.295, K.302, G.306, S.307, M.308, L.311, M.312, F.314, D.315, N.373, D.375, A.376, E.377, L.403, T.404, G.405, L.408, S.470, A.493, F.499 Ligands: CO3.36, ZN.37 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.314, E:A.376 Hydrogen bonds: E:K.290, E:K.302, E:D.375, E:D.375, E:L.403, E:G.405 Water bridges: E:S.470 Halogen bonds: E:G.306 J4V.41: 22 residues within 4Å: Chain F: K.290, D.295, K.302, G.306, M.308, L.311, M.312, F.314, D.315, N.373, D.375, A.376, E.377, R.379, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.42, ZN.43 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:F.314, F:N.373, F:A.376 Hydrogen bonds: F:K.290, F:K.302, F:D.375, F:L.403, F:G.405 Water bridges: F:S.470

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

CO3.2: 7 residues within 4Å: Chain A: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J4V.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.290, A:R.379, A:R.379 CO3.12: 6 residues within 4Å: Chain B: A.376, E.377, G.378, R.379, L.403 Ligands: J4V.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.376, B:G.378, B:R.379, B:L.403 CO3.20: 8 residues within 4Å: Chain C: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: J4V.19 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.378, C:R.379, C:R.379, C:R.379 CO3.28: 7 residues within 4Å: Chain D: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J4V.27 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.376, D:G.378, D:R.379, D:L.403 CO3.36: 7 residues within 4Å: Chain E: K.290, A.376, G.378, R.379, L.403, T.404 Ligands: J4V.35 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.378, E:R.379, E:R.379, E:R.379 CO3.42: 8 residues within 4Å: Chain F: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: J4V.41 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.379, F:R.379, F:R.379

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.295, D.375, E.377 Ligands: J4V.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.295, A:D.375, A:D.375, A:E.377, J4V.1 ZN.13: 5 residues within 4Å: Chain B: D.295, K.302, D.375, E.377 Ligands: J4V.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.295, B:D.375, B:D.375, B:E.377, J4V.11 ZN.21: 4 residues within 4Å: Chain C: D.295, D.375, E.377 Ligands: J4V.19 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.295, C:D.375, C:D.375, C:E.377, J4V.19 ZN.29: 5 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: J4V.27 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.295, D:D.375, D:D.375, D:E.377, J4V.27 ZN.37: 5 residues within 4Å: Chain E: D.295, D.375, A.376, E.377 Ligands: J4V.35 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:D.295, E:D.375, E:D.375, E:E.377, J4V.35 ZN.43: 5 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: J4V.41 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:D.295, F:D.375, F:D.375, F:E.377, J4V.41

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

SO4.4: 4 residues within 4Å: Chain A: I.17, E.18, Y.19, N.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.19, A:N.20, A:N.20 SO4.5: 5 residues within 4Å: Chain A: E.41, G.42, L.135, S.136 Chain D: K.80 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.42, A:S.136, A:S.136 Salt bridges: D:K.80 SO4.6: 6 residues within 4Å: Chain A: S.351, K.352 Chain B: S.351, K.352 Chain C: S.351, K.352 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:K.352, A:K.352, C:K.352 Salt bridges: B:K.352, A:K.352, C:K.352 SO4.7: 4 residues within 4Å: Chain A: N.454, N.461, S.465 Chain B: R.502 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:R.502, A:K.456 Salt bridges: B:R.502 Hydrogen bonds: A:N.461, A:N.461, A:S.465 SO4.14: 3 residues within 4Å: Chain B: N.461, S.465 Chain C: R.502 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.461, B:N.461 Water bridges: B:K.456 Salt bridges: C:R.502 SO4.22: 3 residues within 4Å: Chain A: R.502 Chain C: N.461, S.465 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.461, C:S.465, C:S.465 Water bridges: C:K.456, C:S.466 Salt bridges: A:R.502 SO4.23: 4 residues within 4Å: Chain C: E.18, Y.19, N.20 Ligands: 1PE.26 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.19, C:N.20, C:N.20, C:N.20 SO4.24: 5 residues within 4Å: Chain C: I.445, I.446, N.447, E.448 Chain D: Y.415 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.415, C:N.447, C:N.447, C:E.448 SO4.30: 5 residues within 4Å: Chain D: I.17, E.18, Y.19, N.20 Ligands: 1PE.33 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.19, D:N.20, D:N.20, D:N.20 SO4.31: 3 residues within 4Å: Chain D: R.502 Chain F: N.461, S.465 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:N.461, F:S.465 Water bridges: F:E.370, F:N.461, F:S.465, F:S.465, F:S.465, F:S.465, D:R.502 Salt bridges: D:R.502 SO4.32: 6 residues within 4Å: Chain D: S.351, K.352 Chain E: S.351, K.352 Chain F: S.351, K.352 7 PLIP interactions: 2 interactions with chain F, 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: F:S.351, F:K.352, D:K.352, E:S.351, E:K.352 Salt bridges: D:K.352, E:K.352 SO4.38: 5 residues within 4Å: Chain B: S.115, Y.415 Chain E: I.446, N.447, E.448 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:N.447, E:N.447, E:E.448, B:S.115, B:Y.415 SO4.39: 4 residues within 4Å: Chain E: I.17, E.18, Y.19, N.20 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.19, E:N.20, E:N.20 SO4.44: 3 residues within 4Å: Chain E: N.461, S.465 Chain F: R.502 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:N.461, E:S.465 Water bridges: E:N.461, E:S.465 Salt bridges: F:R.502 SO4.45: 5 residues within 4Å: Chain F: I.17, E.18, Y.19, N.20 Ligands: 1PE.49 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.19, F:N.20, F:N.20

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 4 residues within 4Å: Chain A: G.306, S.307, M.308, D.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.306 DMS.15: 5 residues within 4Å: Chain B: I.17, E.18, Y.19, N.20 Ligands: 1PE.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.19, B:N.20 DMS.16: 5 residues within 4Å: Chain B: P.305, G.306, S.307, M.308, I.309 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.306, B:M.308 DMS.17: 5 residues within 4Å: Chain B: G.245, V.246, K.247, E.248, K.269 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.246, B:K.269

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

1PE.9: 6 residues within 4Å: Chain A: Y.31, G.36, N.38, E.40, N.65, Y.186 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.31 Hydrogen bonds: A:N.38, A:N.65, A:Y.186, A:Y.186 1PE.10: 5 residues within 4Å: Chain A: Y.19, N.20, H.24, K.236, Y.327 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.236 1PE.18: 4 residues within 4Å: Chain B: Y.19, E.232, K.236 Ligands: DMS.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.236 1PE.25: 6 residues within 4Å: Chain C: Y.19, N.20, H.24, F.205, K.236, Y.327 No protein-ligand interaction detected (PLIP) 1PE.26: 4 residues within 4Å: Chain C: Y.19, E.232, K.236 Ligands: SO4.23 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.236 Hydrogen bonds: C:K.236 1PE.33: 5 residues within 4Å: Chain D: Y.19, E.232, K.236 Ligands: SO4.30, 1PE.34 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.235, D:K.236 1PE.34: 6 residues within 4Å: Chain D: Y.19, H.24, F.205, K.236, Y.327 Ligands: 1PE.33 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.236 1PE.48: 5 residues within 4Å: Chain F: Y.19, N.20, H.24, K.236, Y.327 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.327 1PE.49: 4 residues within 4Å: Chain F: Y.19, E.232, K.236 Ligands: SO4.45 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:K.236 Hydrogen bonds: F:K.236

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

EDO.40: 3 residues within 4Å: Chain E: Y.19, F.205, Y.327 3 PLIP interactions: 3 interactions with chain E Water bridges: E:Y.327, E:Y.327, E:Y.327 EDO.46: 4 residues within 4Å: Chain F: G.245, V.246, K.247, E.248 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.245, F:V.246, F:K.247, F:E.248, F:E.248, F:E.248 EDO.47: 4 residues within 4Å: Chain F: S.465, S.466, V.467, K.468 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.468, F:K.468 Water bridges: F:S.464

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vinh, N.B. et al., Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. (2019)

Release Date

2018-12-26

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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