- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x CO3: CARBONATE ION(Non-functional Binders)
CO3.2: 7 residues within 4Å:- Chain A: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TL.8
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:K.293, A:A.379, A:G.381, A:R.382, A:L.406
CO3.11: 8 residues within 4Å:- Chain B: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: ZN.10, 4TL.13
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:G.381, B:R.382, B:R.382, B:R.382
CO3.17: 7 residues within 4Å:- Chain C: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TL.26
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:A.379, C:G.381, C:R.382, C:L.406
CO3.28: 8 residues within 4Å:- Chain D: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: ZN.27, 4TL.35
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:R.382, D:R.382, D:L.406
CO3.37: 7 residues within 4Å:- Chain E: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TL.44
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:G.381, E:R.382, E:L.406
CO3.47: 7 residues within 4Å:- Chain F: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TL.54
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:R.382, F:R.382, F:L.406
- 13 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 5 residues within 4Å:- Chain A: I.20, E.21, Y.22, N.23
- Ligands: 1PE.6
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.22, A:N.23, A:N.23
SO4.5: 5 residues within 4Å:- Chain A: E.44, G.45, L.138, S.139
- Chain D: K.83
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.45, A:S.139
SO4.19: 6 residues within 4Å:- Chain A: S.354, K.355
- Chain B: S.354, K.355
- Chain C: S.354, K.355
7 PLIP interactions:3 interactions with chain C, 3 interactions with chain B, 1 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
- Water bridges: B:K.355
SO4.20: 5 residues within 4Å:- Chain C: G.45, L.138, S.139, K.140
- Chain E: K.83
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain E- Hydrogen bonds: C:G.45, C:S.139, C:S.139, C:K.140
- Salt bridges: E:K.83
SO4.21: 5 residues within 4Å:- Chain C: N.424, N.425, N.487, T.488, A.489
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.425, C:N.487
SO4.22: 9 residues within 4Å:- Chain C: F.75, N.80, M.81, K.83, F.84
- Chain E: Y.95, M.96, F.97, S.103
4 PLIP interactions:1 interactions with chain E, 3 interactions with chain C- Hydrogen bonds: E:S.103
- Water bridges: C:K.83, C:K.83
- Salt bridges: C:K.83
SO4.23: 5 residues within 4Å:- Chain C: I.20, E.21, Y.22, N.23
- Ligands: 1PE.25
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:Y.22, C:N.23, C:N.23
SO4.30: 5 residues within 4Å:- Chain D: I.20, E.21, Y.22, N.23
- Ligands: 1PE.34
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:Y.22, D:N.23, D:N.23
- Water bridges: D:I.20
SO4.39: 3 residues within 4Å:- Chain E: N.424, T.488, A.489
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:N.425
SO4.40: 5 residues within 4Å:- Chain E: I.20, E.21, Y.22, N.23
- Ligands: 1PE.42
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Y.22, E:N.23
SO4.41: 5 residues within 4Å:- Chain E: S.5, E.6, V.7, T.16, N.231
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:V.7, E:T.16, E:T.16, E:N.231
SO4.49: 6 residues within 4Å:- Chain D: S.354, K.355
- Chain E: S.354, K.355
- Chain F: S.354, K.355
6 PLIP interactions:2 interactions with chain D, 2 interactions with chain F, 2 interactions with chain E- Hydrogen bonds: D:K.355, F:K.355, E:K.355
- Salt bridges: D:K.355, F:K.355, E:K.355
SO4.50: 5 residues within 4Å:- Chain F: S.5, E.6, V.7, T.16, N.231
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:V.7, F:T.16, F:N.231
- Water bridges: F:T.16
- 18 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.6: 5 residues within 4Å:- Chain A: Y.22, N.23, E.235, K.239
- Ligands: SO4.4
Ligand excluded by PLIP1PE.7: 7 residues within 4Å:- Chain A: Y.22, N.23, H.27, F.208, K.239, L.240, Y.330
Ligand excluded by PLIP1PE.14: 4 residues within 4Å:- Chain B: Y.22, E.235, K.239
- Ligands: 1PE.15
Ligand excluded by PLIP1PE.15: 7 residues within 4Å:- Chain B: Y.22, N.23, H.27, K.239, L.240, Y.330
- Ligands: 1PE.14
Ligand excluded by PLIP1PE.24: 7 residues within 4Å:- Chain C: Y.22, N.23, H.27, F.208, K.239, L.240, Y.330
Ligand excluded by PLIP1PE.25: 4 residues within 4Å:- Chain C: Y.22, E.235, K.239
- Ligands: SO4.23
Ligand excluded by PLIP1PE.31: 6 residues within 4Å:- Chain D: Y.22, N.23, H.27, F.208, K.239, Y.330
Ligand excluded by PLIP1PE.32: 5 residues within 4Å:- Chain D: L.433, S.436, K.437, P.442, V.443
Ligand excluded by PLIP1PE.33: 2 residues within 4Å:- Chain D: K.30, H.185
Ligand excluded by PLIP1PE.34: 4 residues within 4Å:- Chain D: Y.22, E.235, K.239
- Ligands: SO4.30
Ligand excluded by PLIP1PE.42: 5 residues within 4Å:- Chain E: Y.22, E.235, Q.238, K.239
- Ligands: SO4.40
Ligand excluded by PLIP1PE.43: 6 residues within 4Å:- Chain E: Y.22, H.27, F.208, K.239, L.240, Y.330
Ligand excluded by PLIP1PE.45: 4 residues within 4Å:- Chain E: S.12, D.14, P.15, T.16
Ligand excluded by PLIP1PE.51: 6 residues within 4Å:- Chain F: Y.22, N.23, H.27, F.208, K.239, Y.330
Ligand excluded by PLIP1PE.52: 4 residues within 4Å:- Chain F: Y.22, N.23, E.235, K.239
Ligand excluded by PLIP1PE.53: 5 residues within 4Å:- Chain D: S.173
- Chain F: N.368, K.370, D.462, Q.486
Ligand excluded by PLIP1PE.55: 4 residues within 4Å:- Chain A: W.444, W.445
- Chain F: W.444, W.445
Ligand excluded by PLIP1PE.56: 6 residues within 4Å:- Chain F: Q.9, S.12, L.13, D.14, P.15, T.16
Ligand excluded by PLIP- 6 x 4TL: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluorobiphenyl-4-yl)ethyl]-2,2-dimethylpropanamide(Non-covalent)
4TL.8: 22 residues within 4Å:- Chain A: K.293, D.298, K.305, G.309, M.311, L.314, M.315, F.317, D.318, D.378, E.380, G.381, L.406, T.407, G.408, L.411, S.473, A.496, F.502
- Ligands: ZN.1, CO3.2, ZN.3
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:F.317
- Hydrogen bonds: A:K.305, A:D.378, A:E.380, A:G.381, A:L.406, A:G.408
- pi-Cation interactions: A:K.305
4TL.13: 20 residues within 4Å:- Chain B: K.293, D.298, K.305, G.309, S.310, M.311, L.314, M.315, D.378, E.380, G.381, L.406, T.407, G.408, L.411, A.496, F.502
- Ligands: ZN.10, CO3.11, ZN.12
8 PLIP interactions:8 interactions with chain B- Hydrogen bonds: B:K.305, B:D.378, B:E.380, B:G.381, B:L.406, B:G.408
- Water bridges: B:S.473
- pi-Cation interactions: B:K.305
4TL.26: 23 residues within 4Å:- Chain C: K.293, D.298, K.305, G.309, S.310, M.311, L.314, M.315, D.318, D.378, E.380, G.381, R.382, L.406, T.407, G.408, L.411, S.473, A.496, F.502
- Ligands: ZN.16, CO3.17, ZN.18
12 PLIP interactions:12 interactions with chain C- Hydrogen bonds: C:K.293, C:D.298, C:K.305, C:D.378, C:E.380, C:G.381, C:L.406, C:G.408
- Water bridges: C:D.378, C:A.409
- pi-Cation interactions: C:K.305
- Halogen bonds: C:G.309
4TL.35: 21 residues within 4Å:- Chain D: K.293, D.298, K.305, G.309, S.310, M.311, L.314, M.315, D.318, D.378, E.380, G.381, L.406, T.407, G.408, L.411, A.496, F.502
- Ligands: ZN.27, CO3.28, ZN.29
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:K.305, D:D.378, D:E.380, D:G.381, D:L.406, D:G.408
- pi-Cation interactions: D:K.305
4TL.44: 21 residues within 4Å:- Chain E: K.293, D.298, K.305, G.309, S.310, M.311, L.314, M.315, D.318, D.378, E.380, G.381, L.406, T.407, G.408, L.411, A.496, F.502
- Ligands: ZN.36, CO3.37, ZN.38
10 PLIP interactions:10 interactions with chain E- Hydrogen bonds: E:K.293, E:D.298, E:K.305, E:D.378, E:E.380, E:G.381, E:L.406, E:G.408
- Water bridges: E:S.473
- Halogen bonds: E:G.309
4TL.54: 20 residues within 4Å:- Chain F: K.293, D.298, K.305, G.309, S.310, M.311, L.314, M.315, D.378, E.380, G.381, L.406, T.407, G.408, L.411, A.496, F.502
- Ligands: ZN.46, CO3.47, ZN.48
8 PLIP interactions:8 interactions with chain F- Hydrogen bonds: F:K.293, F:K.305, F:D.378, F:E.380, F:G.381, F:L.406, F:G.408
- Halogen bonds: F:G.309
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 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
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 13 x SO4: SULFATE ION(Non-functional Binders)
- 18 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 6 x 4TL: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluorobiphenyl-4-yl)ethyl]-2,2-dimethylpropanamide(Non-covalent)
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 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
AB
BC
CD
DE
EF
F