SMTL ID : 6eee.2 (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: 21 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: CO3.2, ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.314, A:A.376 Hydrogen bonds: A:K.290, A:K.302, A:L.403, A:G.405 Halogen bonds: A:G.306 J4V.10: 24 residues within 4Å: Chain B: K.290, D.295, K.302, G.306, S.307, M.308, M.312, F.314, D.315, N.373, D.375, A.376, E.377, R.379, T.402, L.403, T.404, G.405, L.408, S.470, A.493, F.499 Ligands: CO3.11, ZN.12 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.314, B:A.376 Hydrogen bonds: B:K.290, B:K.302, B:D.375, B:D.375, B:G.378, B:L.403, B:G.405 Halogen bonds: B:G.306 J4V.20: 21 residues within 4Å: Chain C: K.290, D.295, K.302, G.306, M.308, M.312, 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: CO3.21, ZN.22, EDO.34 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.376 Hydrogen bonds: C:K.290, C:D.295, C:D.295, C:K.302, C:L.403, C:G.405 Water bridges: C:K.302, C:D.375, C:A.406 Halogen bonds: C:G.306 J4V.29: 21 residues within 4Å: Chain D: K.290, D.295, K.302, G.306, M.308, L.311, 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: CO3.30, ZN.31 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.376 Hydrogen bonds: D:K.290, D:K.302, D:D.375, D:E.377, D:L.403, D:G.405 J4V.40: 22 residues within 4Å: Chain E: K.290, D.295, K.302, G.306, M.308, L.311, M.312, 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: CO3.41, ZN.42 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:A.376 Hydrogen bonds: E:K.290, E:D.295, E:K.302, E:D.375, E:L.403, E:G.405 Halogen bonds: E:G.306 J4V.53: 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, L.403, T.404, G.405, L.408, S.470, A.493, F.499 Ligands: CO3.54, ZN.55 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:F.314, F:A.376 Hydrogen bonds: F:K.290, F:K.302, F:L.403, F:G.405 Halogen bonds: F:G.306

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

CO3.2: 8 residues within 4Å: Chain A: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: J4V.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.379, A:R.379, A:L.403 CO3.11: 7 residues within 4Å: Chain B: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J4V.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.379, B:R.379, B:L.403 CO3.21: 8 residues within 4Å: Chain C: K.290, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: J4V.20 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.378, C:R.379, C:R.379, C:R.379 CO3.30: 7 residues within 4Å: Chain D: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J4V.29 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.376, D:G.378, D:R.379, D:L.403 CO3.41: 7 residues within 4Å: Chain E: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J4V.40 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.379, E:R.379, E:R.379 CO3.54: 7 residues within 4Å: Chain F: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: J4V.53 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.290, F:R.379, F:R.379, F:R.379

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: D.295, K.302, 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.12: 5 residues within 4Å: Chain B: D.295, K.302, D.375, E.377 Ligands: J4V.10 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.10 ZN.22: 5 residues within 4Å: Chain C: D.295, K.302, D.375, E.377 Ligands: J4V.20 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.295, C:D.375, C:D.375, C:E.377 ZN.31: 5 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: J4V.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, J4V.29 ZN.42: 5 residues within 4Å: Chain E: D.295, K.302, D.375, E.377 Ligands: J4V.40 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.295, E:D.375, E:D.375, E:E.377, E:E.377 ZN.55: 5 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: J4V.53 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.53

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

SO4.4: 5 residues within 4Å: Chain A: I.17, E.18, Y.19, N.20 Ligands: 1PE.9 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: N.461, S.465 Chain B: R.502 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain A: S.351, K.352 Chain B: S.351, K.352 Chain C: S.351, K.352 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: I.17, E.18, Y.19, N.20 Ligands: 2PE.16 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: N.461, S.465 Chain C: R.502 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: R.502 Chain C: N.461, S.465 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain C: I.17, E.18, Y.19, N.20 Ligands: 1PE.27 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain C: A.304, P.305, G.306, S.307, M.308, D.310 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain D: Y.19, N.20 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain D: N.461, S.465 Chain E: R.502 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain D: S.351, K.352 Chain E: S.351, K.352 Chain F: S.351, K.352 Ligand excluded by PLIP SO4.44: 5 residues within 4Å: Chain E: I.17, E.18, Y.19, N.20 Ligands: 1PE.51 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain E: G.42, S.100, K.134, L.135, S.136 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain E: N.461, S.465 Chain F: R.502 Ligand excluded by PLIP SO4.56: 3 residues within 4Å: Chain D: R.502 Chain F: N.461, S.465 Ligand excluded by PLIP SO4.57: 4 residues within 4Å: Chain F: E.18, Y.19, N.20 Ligands: 1PE.60 Ligand excluded by PLIP

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

DMS.6: 4 residues within 4Å: Chain A: P.305, G.306, S.307, M.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.306, A:M.308 Water bridges: A:I.309 DMS.19: 4 residues within 4Å: Chain B: A.117, Y.415 Chain E: N.447, E.448 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:N.447, E:N.447, B:Y.415

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

EDO.7: 3 residues within 4Å: Chain A: R.167, K.169, Y.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.220 EDO.18: 3 residues within 4Å: Chain B: L.517, N.518, D.519 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.517 EDO.26: 7 residues within 4Å: Chain C: I.445, I.446, N.447, E.448 Chain D: S.115, A.117, Y.415 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.445, C:N.447, C:N.447, C:E.448, D:S.115, D:Y.415 EDO.34: 4 residues within 4Å: Chain C: L.408 Chain D: S.466, K.468 Ligands: J4V.20 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.466, D:K.468 EDO.35: 4 residues within 4Å: Chain D: S.465, S.466, V.467, K.468 No protein-ligand interaction detected (PLIP) EDO.36: 2 residues within 4Å: Chain D: S.433, V.440 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.415, D:S.433 EDO.47: 4 residues within 4Å: Chain E: H.24, I.26, E.198, R.201 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.198, E:R.201 EDO.48: 5 residues within 4Å: Chain C: H.90 Chain E: S.88, K.89, H.90, M.129 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:H.90, E:H.90 EDO.49: 4 residues within 4Å: Chain E: L.130, H.131, E.178, Y.179 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.179 EDO.50: 4 residues within 4Å: Chain E: G.245, V.246, K.247, E.248 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.245, E:V.246, E:K.247, E:E.248, E:E.248, E:E.248 EDO.58: 5 residues within 4Å: Chain A: Y.415 Chain F: I.445, I.446, N.447, E.448 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain F Water bridges: A:Y.415 Hydrogen bonds: F:I.445, F:N.447, F:N.447, F:E.448

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

1PE.8: 7 residues within 4Å: Chain A: Y.19, N.20, H.24, F.205, K.236, Y.327 Ligands: 1PE.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.236 1PE.9: 5 residues within 4Å: Chain A: Y.19, E.232, K.236 Ligands: SO4.4, 1PE.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.236 Hydrogen bonds: A:E.232, A:K.236 1PE.17: 6 residues within 4Å: Chain B: Y.19, H.24, F.205, K.236, Y.327 Ligands: 2PE.16 No protein-ligand interaction detected (PLIP) 1PE.27: 5 residues within 4Å: Chain C: Y.19, E.232, Q.235, K.236 Ligands: SO4.24 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.236 Hydrogen bonds: C:K.236 1PE.28: 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.37: 6 residues within 4Å: Chain D: Y.19, N.20, H.24, F.205, K.236, Y.327 2 PLIP interactions: 2 interactions with chain D Water bridges: D:Y.327, D:T.331 1PE.38: 3 residues within 4Å: Chain D: Y.19, E.232, K.236 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.232 Hydrogen bonds: D:K.236 1PE.39: 6 residues within 4Å: Chain D: N.365, K.367, D.459, E.480, Q.483 Chain E: S.170 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:S.170, D:K.367, D:Q.483 1PE.51: 7 residues within 4Å: Chain E: Y.19, N.20, E.232, Q.235, K.236 Ligands: SO4.44, 1PE.52 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:K.236 Hydrogen bonds: E:N.20, E:K.236 1PE.52: 8 residues within 4Å: Chain E: Y.19, N.20, H.24, F.205, K.236, L.237, Y.327 Ligands: 1PE.51 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.327 1PE.59: 6 residues within 4Å: Chain D: S.170 Chain F: N.365, K.367, D.459, E.480, Q.483 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.367, F:E.480 1PE.60: 6 residues within 4Å: Chain F: Y.19, E.232, Q.235, K.236 Ligands: SO4.57, 1PE.61 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:K.236 Hydrogen bonds: F:K.236 1PE.61: 6 residues within 4Å: Chain F: Y.19, H.24, F.205, K.236, Y.327 Ligands: 1PE.60 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.19, F:N.20 1PE.62: 5 residues within 4Å: Chain F: S.464, S.465, S.466, V.467, K.468 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.465

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

2PE.16: 5 residues within 4Å: Chain B: Y.19, E.232, K.236 Ligands: SO4.14, 1PE.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.236

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
G

B
H

C
I

D
J

E
K

F
L

M17 LEUCYL-AMINOPEPTIDASE

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