SMTL ID : 4k3n.2 (1 other biounit)

Phosphonic Arginine Mimetics as Inhibitors of the M17 Aminopeptidases from Plasmodium falciparum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: K.291, D.296, D.316, E.378 Ligands: CO3.2, ZN.3, 1OT.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.296, A:D.316, A:E.378 ZN.3: 6 residues within 4Å: Chain A: D.296, K.303, D.376, E.378 Ligands: ZN.1, 1OT.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.296, A:D.376, A:D.376, A:E.378 ZN.12: 7 residues within 4Å: Chain B: K.291, D.296, D.316, E.378 Ligands: CO3.13, ZN.14, 1OT.15 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.296, B:D.316, B:E.378 ZN.14: 6 residues within 4Å: Chain B: D.296, K.303, D.376, E.378 Ligands: ZN.12, 1OT.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.296, B:D.376, B:D.376, B:E.378 ZN.19: 7 residues within 4Å: Chain C: K.291, D.296, D.316, E.378 Ligands: CO3.20, ZN.21, 1OT.22 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.296, C:D.316, C:E.378 ZN.21: 6 residues within 4Å: Chain C: D.296, K.303, D.376, E.378 Ligands: ZN.19, 1OT.22 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.296, C:D.376, C:D.376, C:E.378 ZN.29: 7 residues within 4Å: Chain D: K.291, D.296, D.316, E.378 Ligands: CO3.30, ZN.31, 1OT.32 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.296, D:D.316, D:E.378 ZN.31: 6 residues within 4Å: Chain D: D.296, K.303, D.376, E.378 Ligands: ZN.29, 1OT.32 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.296, D:D.376, D:D.376, D:E.378 ZN.39: 7 residues within 4Å: Chain E: K.291, D.296, D.316, E.378 Ligands: CO3.40, ZN.41, 1OT.42 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.296, E:D.316, E:E.378 ZN.41: 6 residues within 4Å: Chain E: D.296, K.303, D.376, E.378 Ligands: ZN.39, 1OT.42 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.296, E:D.376, E:D.376, E:E.378 ZN.49: 7 residues within 4Å: Chain F: K.291, D.296, D.316, E.378 Ligands: CO3.50, ZN.51, 1OT.52 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.296, F:D.316, F:E.378 ZN.51: 6 residues within 4Å: Chain F: D.296, K.303, D.376, E.378 Ligands: ZN.49, 1OT.52 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.296, F:D.376, F:D.376, F:E.378

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

CO3.2: 9 residues within 4Å: Chain A: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.1, 1OT.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.379, A:R.380, A:R.380, A:R.380 CO3.13: 9 residues within 4Å: Chain B: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.12, 1OT.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.378, B:G.379, B:R.380, B:R.380, B:R.380 CO3.20: 9 residues within 4Å: Chain C: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.19, 1OT.22 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.377, C:G.379, C:R.380, C:L.404 CO3.30: 9 residues within 4Å: Chain D: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.29, 1OT.32 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.376, D:G.379, D:R.380 CO3.40: 9 residues within 4Å: Chain E: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.39, 1OT.42 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.378, E:R.380, E:R.380, E:R.380 CO3.50: 9 residues within 4Å: Chain F: K.291, D.376, A.377, E.378, G.379, R.380, L.404 Ligands: ZN.49, 1OT.52 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.291, F:G.379, F:R.380, F:L.404

6 x 1OT: {(R)-amino[4-(1H-pyrazol-1-yl)phenyl]methyl}phosphonic acid(Non-covalent)

1OT.4: 17 residues within 4Å: Chain A: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494 Ligands: ZN.1, CO3.2, ZN.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.315, A:L.409, A:A.494 Hydrogen bonds: A:K.303, A:D.316, A:D.376, A:D.376 Water bridges: A:R.380 1OT.15: 16 residues within 4Å: Chain B: K.291, D.296, K.303, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494 Ligands: ZN.12, CO3.13, ZN.14 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.315, B:L.409, B:A.494 Hydrogen bonds: B:K.291, B:K.303, B:D.316, B:D.376, B:D.376 Water bridges: B:R.380 1OT.22: 17 residues within 4Å: Chain C: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494 Ligands: ZN.19, CO3.20, ZN.21 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.315, C:L.409, C:A.494 Hydrogen bonds: C:K.291, C:K.291, C:K.303, C:D.376, C:D.376 1OT.32: 17 residues within 4Å: Chain D: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494 Ligands: ZN.29, CO3.30, ZN.31 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.315, D:L.409 Hydrogen bonds: D:K.303, D:D.316, D:D.376 Water bridges: D:R.380 1OT.42: 17 residues within 4Å: Chain E: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494 Ligands: ZN.39, CO3.40, ZN.41 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:F.315, E:L.409, E:A.494 Hydrogen bonds: E:K.291, E:K.291, E:K.303, E:D.376, E:D.376 Water bridges: E:G.406 1OT.52: 17 residues within 4Å: Chain F: K.291, D.296, K.303, M.309, M.313, F.315, D.316, D.376, E.378, T.403, L.404, G.406, L.409, A.494 Ligands: ZN.49, CO3.50, ZN.51 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:F.315, F:L.409, F:A.494 Hydrogen bonds: F:K.303, F:D.316, F:D.376, F:D.376 Water bridges: F:R.380

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

SO4.5: 9 residues within 4Å: Chain A: F.73, N.78, K.81, F.82, F.92 Chain D: Y.93, M.94, F.95, S.101 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.101 Salt bridges: A:K.81 SO4.6: 5 residues within 4Å: Chain A: I.18, E.19, Y.20, N.21 Ligands: 1PE.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.20, A:N.21, A:N.21 SO4.7: 5 residues within 4Å: Chain A: E.42, G.43, L.136, S.137 Chain D: K.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.43, A:S.137 SO4.16: 6 residues within 4Å: Chain A: S.352, K.353 Chain B: S.352, K.353 Chain C: S.352, K.353 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:K.353, C:K.353, A:K.353 Salt bridges: B:K.353, C:K.353 SO4.23: 5 residues within 4Å: Chain C: I.18, E.19, Y.20, N.21 Ligands: 1PE.25 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.20, C:N.21, C:N.21 SO4.24: 8 residues within 4Å: Chain C: F.73, N.78, M.79, K.81 Chain E: Y.93, M.94, F.95, S.101 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain E Salt bridges: C:K.81 Hydrogen bonds: E:S.101, E:S.101 SO4.33: 5 residues within 4Å: Chain D: I.18, E.19, Y.20, N.21 Ligands: 1PE.35 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.20, D:N.21 SO4.43: 6 residues within 4Å: Chain D: S.352, K.353 Chain E: S.352, K.353 Chain F: S.352, K.353 6 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, 2 interactions with chain D Hydrogen bonds: E:K.353, F:K.353, D:K.353 Salt bridges: E:K.353, F:K.353, D:K.353 SO4.44: 5 residues within 4Å: Chain E: I.18, E.19, Y.20, N.21 Ligands: 1PE.45 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.20, E:N.21 SO4.53: 5 residues within 4Å: Chain F: I.18, E.19, Y.20, N.21 Ligands: 1PE.57 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.20, F:N.21, F:N.21

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

1PE.8: 7 residues within 4Å: Chain A: Y.20, N.21, H.25, F.206, K.237, Y.328 Ligands: 1PE.11 Ligand excluded by PLIP 1PE.9: 5 residues within 4Å: Chain A: Y.32, N.39, E.41, Y.187 Ligands: 1PE.10 Ligand excluded by PLIP 1PE.10: 2 residues within 4Å: Chain A: N.39 Ligands: 1PE.9 Ligand excluded by PLIP 1PE.11: 7 residues within 4Å: Chain A: Y.20, N.21, E.233, Q.236, K.237 Ligands: SO4.6, 1PE.8 Ligand excluded by PLIP 1PE.25: 7 residues within 4Å: Chain C: Y.20, N.21, E.233, Q.236, K.237 Ligands: SO4.23, 1PE.26 Ligand excluded by PLIP 1PE.26: 7 residues within 4Å: Chain C: Y.20, N.21, H.25, F.206, K.237, Y.328 Ligands: 1PE.25 Ligand excluded by PLIP 1PE.27: 5 residues within 4Å: Chain C: I.446, I.447, N.448, E.449 Chain D: Y.416 Ligand excluded by PLIP 1PE.34: 7 residues within 4Å: Chain D: Y.20, N.21, H.25, F.206, K.237, L.238, Y.328 Ligand excluded by PLIP 1PE.35: 5 residues within 4Å: Chain D: Y.20, E.233, Q.236, K.237 Ligands: SO4.33 Ligand excluded by PLIP 1PE.36: 7 residues within 4Å: Chain D: N.366, K.368, R.451, D.460, E.481, Q.484 Chain E: S.171 Ligand excluded by PLIP 1PE.37: 7 residues within 4Å: Chain C: W.442, W.443 Chain D: L.431, K.435, V.441, W.442, W.443 Ligand excluded by PLIP 1PE.45: 6 residues within 4Å: Chain E: Y.20, E.233, Q.236, K.237 Ligands: SO4.44, 1PE.46 Ligand excluded by PLIP 1PE.46: 7 residues within 4Å: Chain E: Y.20, H.25, F.206, K.237, L.238, Y.328 Ligands: 1PE.45 Ligand excluded by PLIP 1PE.47: 6 residues within 4Å: Chain E: N.366, K.368, R.451, D.460, E.481 Chain F: S.171 Ligand excluded by PLIP 1PE.48: 6 residues within 4Å: Chain E: Q.7, S.10, L.11, D.12, P.13, T.14 Ligand excluded by PLIP 1PE.54: 6 residues within 4Å: Chain F: Y.20, N.21, H.25, F.206, K.237, Y.328 Ligand excluded by PLIP 1PE.55: 7 residues within 4Å: Chain D: S.171 Chain F: N.366, K.368, R.451, D.460, E.481, Q.484 Ligand excluded by PLIP 1PE.56: 4 residues within 4Å: Chain F: S.434, K.435, V.441, W.442 Ligand excluded by PLIP 1PE.57: 5 residues within 4Å: Chain F: Y.20, N.21, E.233, K.237 Ligands: SO4.53 Ligand excluded by PLIP

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

2PE.17: 6 residues within 4Å: Chain B: Y.20, N.21, H.25, F.206, K.237, Y.328 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.25, B:Y.328 2PE.18: 4 residues within 4Å: Chain B: Y.32, N.39, N.66, Y.187 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.32 Hydrogen bonds: B:N.39, B:Y.187 2PE.28: 6 residues within 4Å: Chain C: Y.32, G.36, G.37, N.39, N.66, Y.187 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.39, C:Y.187 2PE.38: 5 residues within 4Å: Chain D: D.396, N.422, N.423, T.486, A.487 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kannan Sivaraman, K. et al., Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum. J.Med.Chem. (2013)

Release Date

2013-06-12

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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