SMTL ID : 4x2t.2 (1 other biounit)

X-ray crystal structure of the orally available aminopeptidase inhibitor, Tosedostat, bound to the M17 Leucyl Aminopeptidase from P. falciparum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.295, D.375, E.377 Ligands: ZN.2, TOD.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.295, A:D.295, A:D.375, A:D.375, A:E.377 ZN.2: 7 residues within 4Å: Chain A: K.290, D.295, D.315, E.377 Ligands: ZN.1, TOD.3, CO3.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.295, A:D.315, A:E.377, H2O.2 ZN.9: 7 residues within 4Å: Chain B: K.290, D.295, D.315, E.377 Ligands: ZN.10, TOD.11, CO3.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.295, B:D.315, B:E.377, H2O.6 ZN.10: 5 residues within 4Å: Chain B: D.295, D.375, E.377 Ligands: ZN.9, TOD.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.295, B:D.375, B:D.375, B:E.377 ZN.14: 6 residues within 4Å: Chain C: D.295, D.375, E.377 Ligands: ZN.15, TOD.16, CO3.17 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.295, C:D.295, C:D.375, C:D.375, C:E.377 ZN.15: 7 residues within 4Å: Chain C: K.290, D.295, D.315, E.377 Ligands: ZN.14, TOD.16, CO3.17 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.295, C:D.315, C:E.377, H2O.8 ZN.19: 6 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: ZN.20, TOD.21 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.295, D:D.295, D:D.375, D:D.375, D:E.377 ZN.20: 7 residues within 4Å: Chain D: K.290, D.295, D.315, E.377 Ligands: ZN.19, TOD.21, CO3.22 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.295, D:D.315, D:E.377 ZN.23: 5 residues within 4Å: Chain E: D.295, D.375, E.377 Ligands: ZN.24, TOD.25 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.295, E:D.375, E:D.375, E:E.377 ZN.24: 6 residues within 4Å: Chain E: K.290, D.295, D.315, E.377 Ligands: ZN.23, TOD.25 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.295, E:D.315, E:E.377 ZN.27: 5 residues within 4Å: Chain F: D.295, D.375, E.377 Ligands: ZN.28, TOD.29 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.295, F:D.295, F:D.375, F:D.375, F:E.377 ZN.28: 7 residues within 4Å: Chain F: K.290, D.295, D.315, E.377 Ligands: ZN.27, TOD.29, CO3.30 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.295, F:D.315, F:E.377

6 x TOD: (2S)-({(2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}amino)(phenyl)ethanoic acid(Non-covalent)

TOD.3: 14 residues within 4Å: Chain A: K.290, D.295, K.302, N.373, D.375, E.377, L.403, T.404, G.405, Y.409, I.463 Ligands: ZN.1, ZN.2, CO3.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.409, A:I.463 Hydrogen bonds: A:K.302, A:E.377, A:L.403, A:G.405 Water bridges: A:A.406 TOD.11: 13 residues within 4Å: Chain B: K.290, D.295, K.302, D.315, N.373, D.375, A.376, E.377, L.403, G.405 Ligands: ZN.9, ZN.10, CO3.12 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.375 Hydrogen bonds: B:K.302, B:T.402, B:G.405 TOD.16: 15 residues within 4Å: Chain C: K.290, D.295, K.302, D.375, A.376, E.377, R.379, L.403, T.404, G.405, A.406, S.470 Ligands: ZN.14, ZN.15, CO3.17 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.376, C:A.406 Hydrogen bonds: C:K.290, C:D.295, C:K.302, C:L.403, C:G.405, C:A.406 TOD.21: 14 residues within 4Å: Chain C: Y.409 Chain D: K.290, D.295, K.302, D.315, D.375, E.377, T.402, L.403, T.404, G.405 Ligands: ZN.19, ZN.20, CO3.22 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.302, D:G.378, D:L.403, D:G.405, D:A.406 Hydrophobic interactions: C:Y.409 TOD.25: 17 residues within 4Å: Chain B: Y.409 Chain E: K.290, D.295, K.302, N.373, D.375, A.376, E.377, R.379, L.403, T.404, G.405, A.406, Y.409 Ligands: ZN.23, ZN.24, CO3.26 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:A.376, E:Y.409, B:Y.409 Hydrogen bonds: E:K.302, E:L.403, E:G.405 TOD.29: 15 residues within 4Å: Chain F: K.290, D.295, K.302, G.306, D.315, D.375, E.377, R.379, L.403, T.404, G.405, S.470 Ligands: ZN.27, ZN.28, CO3.30 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:K.302, F:L.403, F:G.405, F:A.406, F:S.470

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

CO3.4: 9 residues within 4Å: Chain A: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.2, TOD.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.376, A:G.378, A:R.379 CO3.12: 9 residues within 4Å: Chain B: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.9, TOD.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.378, B:R.379, B:R.379, B:R.379 CO3.17: 11 residues within 4Å: Chain C: K.290, D.375, A.376, E.377, G.378, R.379, L.403, T.404 Ligands: ZN.14, ZN.15, TOD.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.377, C:G.378, C:R.379, C:R.379, C:R.379 CO3.22: 9 residues within 4Å: Chain D: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.20, TOD.21 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.377, D:G.378, D:R.379, D:R.379 CO3.26: 8 residues within 4Å: Chain E: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: TOD.25 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.377, E:G.378, E:R.379, E:R.379, E:L.403 CO3.30: 9 residues within 4Å: Chain F: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.28, TOD.29 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.377, F:G.378, F:R.379, F:R.379, F:R.379

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

SO4.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.6: 6 residues within 4Å: Chain A: G.42, K.134, L.135, S.136, K.137 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:K.137 Salt bridges: D:K.80 SO4.18: 6 residues within 4Å: Chain A: S.351, K.352 Chain B: S.351, K.352 Chain C: S.351, K.352 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:K.352, B:K.352, C:K.352 Salt bridges: B:K.352, C:K.352 SO4.31: 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: 2 interactions with chain E, 2 interactions with chain F, 2 interactions with chain D Hydrogen bonds: E:K.352, F:K.352, D:K.352 Salt bridges: E:K.352, F:K.352, D:K.352 SO4.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

1PE.7: 5 residues within 4Å: Chain A: Y.19, N.20, H.24, K.236, Y.327 No protein-ligand interaction detected (PLIP) 1PE.8: 4 residues within 4Å: Chain A: Y.19, E.232, Q.235, K.236 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.236 Hydrogen bonds: A:K.236 1PE.13: 7 residues within 4Å: Chain B: Y.19, N.20, H.24, F.205, K.236, L.237, Y.327 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drinkwater, N. et al., X-ray crystal structures of an orally available aminopeptidase inhibitor, Tosedostat, bound to anti-malarial drug targets PfA-M1 and PfA-M17. Proteins (2015)

Release Date

2015-02-18

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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