SMTL ID : 4zx8.2 (1 other biounit)

X-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 9b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

6 x 4TY: tert-butyl [(1R)-1-(4-bromophenyl)-2-(hydroxyamino)-2-oxoethyl]carbamate(Non-covalent)

4TY.1: 18 residues within 4Å: Chain A: K.293, D.298, K.305, M.311, F.317, N.376, D.378, E.380, G.381, T.405, L.406, T.407, G.408, S.473, A.496 Ligands: ZN.2, ZN.3, CO3.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.317, A:A.496 Hydrogen bonds: A:K.305, A:E.380, A:G.381, A:L.406, A:G.408 Water bridges: A:S.473 4TY.7: 18 residues within 4Å: Chain B: K.293, D.298, K.305, M.311, F.317, N.376, D.378, A.379, E.380, R.382, T.405, L.406, T.407, G.408, A.496 Ligands: ZN.8, ZN.9, CO3.10 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.317, B:A.379, B:A.496 Hydrogen bonds: B:K.305, B:G.381, B:L.406 Water bridges: B:G.408, B:G.408 4TY.14: 16 residues within 4Å: Chain C: K.293, D.298, K.305, F.317, N.376, D.378, E.380, G.381, T.405, L.406, T.407, G.408, A.496 Ligands: ZN.15, ZN.16, CO3.17 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.317, C:A.496 Hydrogen bonds: C:K.293, C:K.305, C:G.381, C:L.406 Water bridges: C:D.378, C:S.473 4TY.21: 16 residues within 4Å: Chain D: K.293, D.298, K.305, M.311, F.317, N.376, D.378, E.380, T.405, L.406, T.407, G.408, A.496 Ligands: ZN.22, ZN.23, CO3.24 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.317, D:A.496 Hydrogen bonds: D:K.305, D:G.381, D:L.406, D:G.408 Water bridges: D:K.305, D:D.378 4TY.30: 18 residues within 4Å: Chain E: K.293, D.298, K.305, M.311, F.317, N.376, D.378, E.380, G.381, R.382, T.405, L.406, T.407, G.408, A.496 Ligands: ZN.31, ZN.32, CO3.33 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:A.496 Hydrogen bonds: E:K.293, E:D.298, E:K.305, E:E.380, E:G.381, E:L.406, E:G.408 Water bridges: E:S.473 4TY.38: 16 residues within 4Å: Chain F: K.293, D.298, K.305, F.317, N.376, D.378, E.380, R.382, T.405, L.406, T.407, G.408, A.496 Ligands: ZN.39, ZN.40, CO3.41 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:N.376, F:A.496 Hydrogen bonds: F:K.305, F:G.381, F:L.406, F:G.408 Water bridges: F:S.473

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: K.293, D.298, D.318, E.380 Ligands: 4TY.1, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.298, A:D.318, A:D.318, A:E.380 ZN.3: 6 residues within 4Å: Chain A: D.298, K.305, D.378, E.380 Ligands: 4TY.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.298, A:D.378, A:D.378, A:E.380 ZN.8: 6 residues within 4Å: Chain B: K.293, D.298, D.318, E.380 Ligands: 4TY.7, ZN.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.298, B:D.318, B:E.380, H2O.8 ZN.9: 6 residues within 4Å: Chain B: D.298, K.305, D.378, E.380 Ligands: 4TY.7, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.298, B:D.378, B:D.378, B:E.380 ZN.15: 6 residues within 4Å: Chain C: D.298, K.305, D.378, E.380 Ligands: 4TY.14, ZN.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.298, C:D.378, C:D.378, C:E.380 ZN.16: 6 residues within 4Å: Chain C: K.293, D.298, D.318, E.380 Ligands: 4TY.14, ZN.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.298, C:D.318, C:E.380 ZN.22: 6 residues within 4Å: Chain D: D.298, K.305, D.378, E.380 Ligands: 4TY.21, ZN.23 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.298, D:D.378, D:D.378, D:E.380 ZN.23: 6 residues within 4Å: Chain D: K.293, D.298, D.318, E.380 Ligands: 4TY.21, ZN.22 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.298, D:D.318, D:D.318, D:E.380 ZN.31: 5 residues within 4Å: Chain E: D.298, D.378, E.380 Ligands: 4TY.30, ZN.32 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.298, E:D.378, E:D.378, E:E.380 ZN.32: 6 residues within 4Å: Chain E: K.293, D.298, D.318, E.380 Ligands: 4TY.30, ZN.31 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.298, E:D.318, E:E.380 ZN.39: 6 residues within 4Å: Chain F: K.293, D.298, D.318, E.380 Ligands: 4TY.38, ZN.40 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.298, F:D.318, F:D.318, F:E.380, H2O.33 ZN.40: 6 residues within 4Å: Chain F: D.298, K.305, D.378, E.380 Ligands: 4TY.38, ZN.39 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.298, F:D.378, F:D.378, F:E.380

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

CO3.4: 8 residues within 4Å: Chain A: K.293, A.379, E.380, G.381, R.382, L.406, T.407 Ligands: 4TY.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.293, A:G.381, A:R.382, A:R.382, A:R.382 CO3.10: 8 residues within 4Å: Chain B: K.293, A.379, E.380, G.381, R.382, L.406, T.407 Ligands: 4TY.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.381, B:R.382, B:R.382, B:R.382 CO3.17: 8 residues within 4Å: Chain C: K.293, A.379, E.380, G.381, R.382, L.406, T.407 Ligands: 4TY.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.379, C:G.381, C:R.382, C:L.406 CO3.24: 7 residues within 4Å: Chain D: K.293, A.379, E.380, G.381, R.382, L.406 Ligands: 4TY.21 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.382, D:R.382, D:L.406 CO3.33: 7 residues within 4Å: Chain E: K.293, A.379, E.380, G.381, R.382, L.406 Ligands: 4TY.30 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.382, E:R.382, E:L.406 CO3.41: 7 residues within 4Å: Chain F: K.293, A.379, E.380, G.381, R.382, L.406 Ligands: 4TY.38 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.382, F:R.382, F:L.406

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

1PE.5: 6 residues within 4Å: Chain A: Y.22, N.23, H.27, K.239, L.240, Y.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.239, A:Y.330 1PE.6: 5 residues within 4Å: Chain A: Y.22, N.23, E.235, Q.238, K.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.239 1PE.11: 5 residues within 4Å: Chain B: Y.22, H.27, K.239, Y.330 Ligands: 1PE.12 No protein-ligand interaction detected (PLIP) 1PE.12: 4 residues within 4Å: Chain B: Y.22, E.235, K.239 Ligands: 1PE.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.239 Hydrogen bonds: B:K.239 1PE.19: 5 residues within 4Å: Chain C: Y.22, E.235, Q.238, K.239 Ligands: 1PE.20 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.238, C:K.239 Hydrogen bonds: C:K.239 1PE.20: 7 residues within 4Å: Chain C: Y.22, N.23, H.27, F.208, K.239, Y.330 Ligands: 1PE.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.330 1PE.25: 6 residues within 4Å: Chain D: Y.22, N.23, E.235, Q.238, K.239 Ligands: SO4.28 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Q.238 Hydrogen bonds: D:N.23, D:K.239 1PE.26: 5 residues within 4Å: Chain D: Y.22, H.27, F.208, K.239, Y.330 No protein-ligand interaction detected (PLIP) 1PE.34: 4 residues within 4Å: Chain E: Y.22, E.235, K.239 Ligands: SO4.37 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.239 1PE.35: 4 residues within 4Å: Chain E: Y.22, H.27, K.239, Y.330 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.239 1PE.42: 5 residues within 4Å: Chain F: Y.22, N.23, H.27, K.239, Y.330 No protein-ligand interaction detected (PLIP)

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

SO4.13: 6 residues within 4Å: Chain A: S.354, K.355 Chain B: S.354, K.355 Chain C: S.354, K.355 8 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:S.354, C:K.355, B:S.354, B:K.355, A:K.355 Salt bridges: C:K.355, B:K.355, A:K.355 SO4.27: 8 residues within 4Å: Chain A: F.75, N.80, F.84, F.94 Chain D: Y.95, M.96, F.97, S.103 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.103, D:S.103 SO4.28: 5 residues within 4Å: Chain D: I.20, E.21, Y.22, N.23 Ligands: 1PE.25 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.22, D:N.23, D:N.23 SO4.29: 4 residues within 4Å: Chain D: P.308, G.309, S.310, M.311 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.309, D:S.310, D:M.311 SO4.36: 6 residues within 4Å: Chain D: S.354, K.355 Chain E: S.354, K.355 Chain F: S.354, K.355 7 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: D:S.354, D:K.355, F:K.355, E:K.355 Salt bridges: D:K.355, F:K.355, E:K.355 SO4.37: 5 residues within 4Å: Chain E: I.20, E.21, Y.22, N.23 Ligands: 1PE.34 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.22, E:N.23

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 6 residues within 4Å: Chain C: I.448, I.449, N.450, E.451 Chain D: S.118, Y.418 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.448, C:N.450, C:E.451, D:S.118, D:Y.418 Water bridges: C:N.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drinkwater, N. et al., Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions. Eur.J.Med.Chem. (2016)

Release Date

2016-03-30

Peptides

Probable M17 family aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

Probable M17 family aminopeptidase

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