SMTL ID : 6ee2.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

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

CO3.1: 6 residues within 4Å: Chain A: K.290, A.376, G.378, R.379, L.403 Ligands: J1V.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.379, A:R.379, A:L.403 CO3.12: 7 residues within 4Å: Chain B: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J1V.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.290, B:R.379, B:R.379 CO3.18: 8 residues within 4Å: Chain C: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: J1V.19 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.378, C:R.379, C:R.379, C:R.379 CO3.27: 7 residues within 4Å: Chain D: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J1V.29 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.376, D:G.378, D:R.379, D:L.403 CO3.34: 8 residues within 4Å: Chain E: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: J1V.36 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.378, E:R.379, E:R.379, E:R.379 CO3.46: 7 residues within 4Å: Chain F: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J1V.48 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.378, F:R.379, F:R.379, F:R.379

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.295, K.302, D.375, E.377 Ligands: J1V.3 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, J1V.3 ZN.13: 4 residues within 4Å: Chain B: D.295, D.375, E.377 Ligands: J1V.14 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, J1V.14 ZN.17: 5 residues within 4Å: Chain C: D.295, K.302, D.375, E.377 Ligands: J1V.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, J1V.19 ZN.28: 4 residues within 4Å: Chain D: D.295, D.375, E.377 Ligands: J1V.29 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, J1V.29 ZN.35: 5 residues within 4Å: Chain E: D.295, K.302, D.375, E.377 Ligands: J1V.36 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, J1V.36 ZN.47: 5 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: J1V.48 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.295, F:D.375, F:D.375, F:E.377

6 x J1V: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]cyclohexanecarboxamide(Non-covalent)

J1V.3: 22 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, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.1, ZN.2, SO4.54 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.314, A:A.376 Hydrogen bonds: A:K.290, A:K.302, A:D.375, A:L.403, A:G.405 Water bridges: A:A.406 Halogen bonds: A:G.306 J1V.14: 19 residues within 4Å: Chain B: K.290, D.295, K.302, G.306, M.308, F.314, D.315, N.373, D.375, A.376, E.377, 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:F.314, B:A.376 Hydrogen bonds: B:K.290, B:K.302, B:D.375, B:E.377, B:L.403, B:G.405 Halogen bonds: B:G.306 J1V.19: 21 residues within 4Å: Chain C: K.290, D.295, K.302, G.306, M.308, L.311, M.312, F.314, D.315, N.373, D.375, E.377, L.403, T.404, G.405, L.408, S.470, A.493, F.499 Ligands: ZN.17, CO3.18 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.314 Hydrogen bonds: C:K.290, C:K.302, C:D.375, C:G.378, C:L.403, C:G.405 Water bridges: C:A.406 J1V.29: 20 residues within 4Å: Chain D: K.290, D.295, K.302, G.306, M.308, L.311, F.314, D.315, N.373, D.375, A.376, E.377, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.27, ZN.28 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.314, D:A.376 Hydrogen bonds: D:K.290, D:K.302, D:D.375, D:L.403, D:G.405 J1V.36: 19 residues within 4Å: Chain E: K.290, D.295, K.302, G.306, S.307, M.308, F.314, D.315, N.373, D.375, E.377, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.34, ZN.35 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.314 Hydrogen bonds: E:K.290, E:K.302, E:D.375, E:L.403, E:G.405 Water bridges: E:A.406 Halogen bonds: E:G.306 J1V.48: 20 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, E.377, L.403, T.404, G.405, L.408, A.493, F.499 Ligands: CO3.46, ZN.47 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.314 Hydrogen bonds: F:K.290, F:D.295, F:K.302, F:L.403, F:G.405 Water bridges: F:K.302 Halogen bonds: F:G.306

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

SO4.4: 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 C, 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:K.352, B:K.352, A:K.352 Salt bridges: C:K.352, B:K.352, A:K.352 SO4.5: 5 residues within 4Å: Chain A: I.17, E.18, Y.19, N.20 Ligands: 1PE.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.19, A:N.20, A:N.20 SO4.11: 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.454, A:N.461, A:S.465 SO4.25: 4 residues within 4Å: Chain B: N.454, N.461, S.465 Chain C: R.502 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.461, B:N.461, B:S.465, B:S.465 Water bridges: C:R.502, C:R.502 Salt bridges: C:R.502 SO4.26: 5 residues within 4Å: Chain C: I.17, E.18, Y.19, N.20 Ligands: 1PE.20 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.19, C:N.20 SO4.37: 5 residues within 4Å: Chain E: I.17, E.18, Y.19, N.20 Ligands: 1PE.38 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Y.19, E:N.20, E:N.20 SO4.43: 8 residues within 4Å: Chain C: F.72, N.77, M.78, K.80, F.81 Chain E: Y.92, M.93, S.100 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:F.72, E:S.100, E:S.100 Salt bridges: C:K.80 SO4.44: 6 residues within 4Å: Chain D: S.351, K.352 Chain E: S.351, K.352 Chain F: S.351, K.352 8 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F, 3 interactions with chain E Hydrogen bonds: D:K.352, F:S.351, F:K.352, E:S.351, E:K.352 Salt bridges: D:K.352, F:K.352, E:K.352 SO4.49: 5 residues within 4Å: Chain F: I.17, E.18, Y.19, N.20 Ligands: 1PE.52 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.19, F:N.20, F:N.20 SO4.54: 3 residues within 4Å: Chain A: F.499 Chain F: K.468 Ligands: J1V.3 2 PLIP interactions: 2 interactions with chain F Water bridges: F:K.468 Salt bridges: F:K.468 SO4.55: 4 residues within 4Å: Chain A: Y.415 Chain F: I.445, I.446, N.447 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.447 Water bridges: F:I.445, F:E.448

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

1PE.6: 6 residues within 4Å: Chain A: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligand excluded by PLIP 1PE.7: 5 residues within 4Å: Chain A: Y.31, N.38, E.40, Y.186 Ligands: 1PE.8 Ligand excluded by PLIP 1PE.8: 4 residues within 4Å: Chain A: G.36, N.38, N.65 Ligands: 1PE.7 Ligand excluded by PLIP 1PE.9: 6 residues within 4Å: Chain A: Y.19, N.20, E.232, Q.235, K.236 Ligands: SO4.5 Ligand excluded by PLIP 1PE.15: 6 residues within 4Å: Chain B: Y.19, H.24, F.205, K.236, L.237, Y.327 Ligand excluded by PLIP 1PE.16: 3 residues within 4Å: Chain B: Y.19, E.232, K.236 Ligand excluded by PLIP 1PE.20: 6 residues within 4Å: Chain C: Y.19, N.20, E.232, K.236 Ligands: 1PE.21, SO4.26 Ligand excluded by PLIP 1PE.21: 7 residues within 4Å: Chain C: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligands: 1PE.20 Ligand excluded by PLIP 1PE.22: 6 residues within 4Å: Chain C: Y.31, G.35, G.36, N.38, N.65, Y.186 Ligand excluded by PLIP 1PE.30: 6 residues within 4Å: Chain D: S.9, L.10, D.11, P.12, T.13, Y.220 Ligand excluded by PLIP 1PE.31: 6 residues within 4Å: Chain D: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligand excluded by PLIP 1PE.32: 3 residues within 4Å: Chain D: Y.19, E.232, K.236 Ligand excluded by PLIP 1PE.38: 6 residues within 4Å: Chain E: Y.19, E.232, Q.235, K.236 Ligands: SO4.37, 1PE.39 Ligand excluded by PLIP 1PE.39: 7 residues within 4Å: Chain E: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligands: 1PE.38 Ligand excluded by PLIP 1PE.40: 6 residues within 4Å: Chain E: N.365, K.367, D.459, E.480, Q.483 Chain F: S.170 Ligand excluded by PLIP 1PE.41: 4 residues within 4Å: Chain E: S.9, D.11, P.12, T.13 Ligand excluded by PLIP 1PE.45: 4 residues within 4Å: Chain A: W.442 Chain F: N.427, L.430, W.442 Ligand excluded by PLIP 1PE.50: 6 residues within 4Å: Chain F: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligand excluded by PLIP 1PE.51: 5 residues within 4Å: Chain D: S.170 Chain F: N.365, K.367, D.459, Q.483 Ligand excluded by PLIP 1PE.52: 4 residues within 4Å: Chain F: Y.19, E.232, K.236 Ligands: SO4.49 Ligand excluded by PLIP 1PE.53: 8 residues within 4Å: Chain D: A.303 Chain F: N.300, L.301, K.302, A.303, A.304, S.307, N.373 Ligand excluded by PLIP

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

DMS.10: 7 residues within 4Å: Chain A: Y.160, D.165, Y.208, S.211, K.503, P.504 Chain C: Y.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.211 Salt bridges: A:D.165 DMS.33: 8 residues within 4Å: Chain A: F.72, N.77, K.80, F.81 Chain D: Y.92, M.93, F.94, S.100 No protein-ligand interaction detected (PLIP) DMS.42: 3 residues within 4Å: Chain E: N.461, S.465 Chain F: R.502 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:N.461, F:R.502 Water bridges: E:K.456

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

EDO.23: 4 residues within 4Å: Chain C: N.421, N.422, T.485, A.486 1 PLIP interactions: 1 interactions with chain C Water bridges: C:A.486 EDO.24: 3 residues within 4Å: Chain C: G.42, L.135, S.136 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.42, C:S.136

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

Pf-M17: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

Pf-M17

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