SMTL ID : 4x2t.1 (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: 6 residues within 4Å: Chain A: D.295, K.302, D.375, E.377 Ligands: ZN.2, TOD.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.295, A:D.375, A:D.375, A:E.377 ZN.2: 6 residues within 4Å: Chain A: K.290, D.295, D.315, E.377 Ligands: ZN.1, TOD.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.295, A:D.315, A:E.377 ZN.10: 5 residues within 4Å: Chain B: D.295, D.375, E.377 Ligands: ZN.11, TOD.12 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.295, B:D.295, B:D.375, B:D.375, B:E.377 ZN.11: 7 residues within 4Å: Chain B: K.290, D.295, D.315, E.377 Ligands: CO3.9, ZN.10, TOD.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.295, B:D.315, B:E.377 ZN.15: 7 residues within 4Å: Chain C: K.290, D.295, D.315, E.377 Ligands: ZN.16, TOD.17, CO3.18 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.295, C:D.315, C:D.315, C:E.377 ZN.16: 6 residues within 4Å: Chain C: D.295, K.302, D.375, E.377 Ligands: ZN.15, TOD.17 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.295, C:D.375, C:D.375, C:E.377 ZN.22: 5 residues within 4Å: Chain D: D.295, K.302, D.375, E.377 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.295, D:D.375, D:D.375, D:E.377 ZN.23: 6 residues within 4Å: Chain D: K.290, D.295, D.315, E.377 Ligands: ZN.22, CO3.24 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.295, D:D.315, D:E.377 ZN.28: 8 residues within 4Å: Chain E: K.290, D.295, D.315, E.377, T.402 Ligands: ZN.29, TOD.30, CO3.31 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.295, E:D.315, E:D.315, E:E.377 ZN.29: 5 residues within 4Å: Chain E: D.295, D.375, E.377 Ligands: ZN.28, TOD.30 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.35: 6 residues within 4Å: Chain F: D.295, K.302, D.375, E.377 Ligands: ZN.36, TOD.37 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.295, F:D.375, F:D.375, F:E.377 ZN.36: 6 residues within 4Å: Chain F: K.290, D.295, D.315, E.377 Ligands: ZN.35, TOD.37 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.295, F:D.315, F:E.377

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

TOD.3: 13 residues within 4Å: Chain A: K.290, D.295, K.302, D.375, A.376, E.377, R.379, L.403, T.404, G.405 Ligands: ZN.1, ZN.2, CO3.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.376 Hydrogen bonds: A:K.302, A:L.403, A:G.405 Water bridges: A:K.302, A:K.302 TOD.12: 12 residues within 4Å: Chain B: K.290, D.295, K.302, G.306, D.375, E.377, L.403, G.405, A.406 Ligands: CO3.9, ZN.10, ZN.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.302, B:E.377, B:L.403, B:G.405 TOD.17: 12 residues within 4Å: Chain C: K.290, D.295, K.302, N.373, D.375, E.377, L.403, T.404, G.405 Ligands: ZN.15, ZN.16, CO3.18 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.290, C:K.302, C:L.403, C:G.405 Water bridges: C:K.302, C:D.375 TOD.30: 15 residues within 4Å: Chain E: K.290, D.295, K.302, D.315, D.375, A.376, E.377, R.379, L.403, T.404, G.405, A.406 Ligands: ZN.28, ZN.29, CO3.31 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:A.376 Hydrogen bonds: E:K.302, E:G.405, E:A.406 TOD.37: 16 residues within 4Å: Chain F: K.290, D.295, K.302, D.315, D.375, A.376, E.377, L.403, T.404, G.405, A.406, Y.409, S.470 Ligands: ZN.35, ZN.36, CO3.38 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:D.375, F:A.406, F:Y.409 Hydrogen bonds: F:K.302, F:L.403, F:T.404, F:G.405 Water bridges: F:K.302, F:D.375

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

CO3.4: 7 residues within 4Å: Chain A: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: TOD.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.290, A:R.379, A:R.379, A:R.379 CO3.9: 8 residues within 4Å: Chain B: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.11, TOD.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.378, B:R.379, B:R.379, B:R.379 CO3.18: 9 residues within 4Å: Chain C: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.15, TOD.17 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 CO3.24: 7 residues within 4Å: Chain D: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.378, D:R.379, D:R.379, D:R.379 CO3.31: 8 residues within 4Å: Chain E: K.290, A.376, E.377, G.378, R.379, L.403 Ligands: ZN.28, TOD.30 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.377, E:R.379, E:R.379, E:R.379 CO3.38: 8 residues within 4Å: Chain F: K.290, D.375, A.376, E.377, G.378, R.379, L.403 Ligands: TOD.37 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.290, F:R.379, F:R.379, F:R.379

8 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: D.165, Y.208, S.211, K.503, P.504 Chain C: Y.457 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Y.457, A:D.165, A:D.165, A:S.211 SO4.7: 4 residues within 4Å: Chain A: I.445, I.446, N.447 Chain F: Y.415 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:I.445, A:N.447, F:Y.415, F:Y.415 Water bridges: A:N.447, A:N.447 SO4.13: 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, 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: A:K.352, C:K.352, B:S.351, B:K.352 Salt bridges: B:K.352 SO4.19: 4 residues within 4Å: Chain C: G.42, K.134, L.135, S.136 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.42, C:K.134, C:S.136 SO4.25: 8 residues within 4Å: Chain A: F.72, N.77, F.81, F.91 Chain D: Y.92, M.93, F.94, S.100 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.100 SO4.32: 6 residues within 4Å: Chain D: S.351, K.352 Chain E: S.351, K.352 Chain F: S.351, K.352 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: D:K.352, E:K.352, F:K.352 Salt bridges: E:K.352, F:K.352 SO4.33: 9 residues within 4Å: Chain C: F.72, N.77, M.78, K.80, F.91 Chain E: Y.92, M.93, F.94, S.100 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Salt bridges: C:K.80 Hydrogen bonds: E:S.100

7 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, L.237, Y.327 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20, A:K.236 1PE.14: 5 residues within 4Å: Chain B: Y.19, H.24, F.205, K.236, Y.327 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.236 1PE.20: 5 residues within 4Å: Chain C: Y.19, E.232, Q.235, K.236 Ligands: 1PE.21 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.236 Hydrogen bonds: C:K.236 1PE.21: 8 residues within 4Å: Chain C: Y.19, N.20, H.24, F.205, K.236, L.237, Y.327 Ligands: 1PE.20 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.20, C:Y.327 1PE.26: 6 residues within 4Å: Chain D: Y.19, N.20, H.24, K.236, Y.327 Ligands: 1PE.27 No protein-ligand interaction detected (PLIP) 1PE.27: 4 residues within 4Å: Chain D: Y.19, E.232, K.236 Ligands: 1PE.26 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.236 1PE.34: 6 residues within 4Å: Chain E: Y.19, H.24, F.205, K.236, L.237, Y.327 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.236

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
A

B
B

C
C

D
D

E
E

F
F

M17 leucyl aminopeptidase

Related Entries With Identical Sequence