- 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: 8 residues within 4Å:- Chain A: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: ZN.1, 4TL.10
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
CO3.14: 7 residues within 4Å:- Chain B: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TL.18
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:G.381, B:R.382, B:R.382, B:R.382
CO3.23: 7 residues within 4Å:- Chain C: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TL.33
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:G.381, C:R.382, C:L.406
CO3.35: 8 residues within 4Å:- Chain D: K.293, A.379, E.380, G.381, R.382, L.406, T.407
- Ligands: 4TL.44
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:R.382, D:R.382, D:L.406
CO3.46: 7 residues within 4Å:- Chain E: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TL.52
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:G.381, E:R.382, E:L.406
CO3.54: 7 residues within 4Å:- Chain F: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TL.60
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:R.382, F:R.382, F:L.406
- 15 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.9
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
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain D- Hydrogen bonds: A:G.45, A:S.139
- Water bridges: D:K.83
SO4.6: 6 residues within 4Å:- Chain A: Y.163, D.168, Y.211, S.214, K.506
- Chain C: Y.460
6 PLIP interactions:1 interactions with chain C, 5 interactions with chain A- Hydrogen bonds: C:Y.460, A:D.168, A:D.168, A:Y.211, A:S.214
- Salt bridges: A:K.506
SO4.16: 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 B, 2 interactions with chain C, 2 interactions with chain A- Hydrogen bonds: B:S.354, B:K.355, C:S.354, C:K.355, A:K.355
- Salt bridges: B:K.355, A:K.355
SO4.17: 5 residues within 4Å:- Chain B: S.5, E.6, V.7, T.16, N.231
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.5, B:V.7, B:N.231
SO4.25: 5 residues within 4Å:- Chain C: I.20, E.21, Y.22, N.23
- Ligands: 1PE.30
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:Y.22, C:N.23, C:N.23, C:N.23
SO4.26: 4 residues within 4Å:- Chain C: E.44, G.45, L.138, S.139
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:G.45, C:S.139, C:S.139
SO4.27: 5 residues within 4Å:- Chain C: S.5, E.6, V.7, T.16, N.231
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:V.7, C:T.16, C:N.231
- Water bridges: C:T.16
SO4.28: 8 residues within 4Å:- Chain C: F.75, N.80, K.83, F.84
- Chain E: Y.95, M.96, F.97, S.103
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain E- Water bridges: C:K.83
- Salt bridges: C:K.83
- Hydrogen bonds: E:S.103
SO4.29: 8 residues within 4Å:- Chain C: L.133, H.134, D.135, N.136, Y.165, N.179, M.180, E.181
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:D.135, C:E.181, C:E.181
- Water bridges: C:D.135, C:N.177, C:N.179
- Salt bridges: C:H.134
SO4.37: 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:2 interactions with chain E, 3 interactions with chain D, 2 interactions with chain F- Hydrogen bonds: E:K.355, D:S.354, D:K.355, F:K.355
- Salt bridges: E:K.355, D:K.355, F:K.355
SO4.38: 5 residues within 4Å:- Chain D: I.20, E.21, Y.22, N.23
- Ligands: 1PE.41
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:I.20, D:Y.22, D:N.23, D:N.23
SO4.39: 7 residues within 4Å:- Chain A: F.75, N.80, F.84
- 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
SO4.48: 5 residues within 4Å:- Chain E: I.20, E.21, Y.22, N.23
- Ligands: 1PE.51
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Y.22, E:N.23
SO4.56: 4 residues within 4Å:- Chain F: E.21, Y.22, N.23
- Ligands: 1PE.62
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:I.20, F:Y.22, F:N.23, F:N.23
- 21 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.7: 5 residues within 4Å:- Chain A: Y.34, N.41, E.43, Y.189
- Ligands: 1PE.8
Ligand excluded by PLIP1PE.8: 3 residues within 4Å:- Chain A: G.39, N.41
- Ligands: 1PE.7
Ligand excluded by PLIP1PE.9: 4 residues within 4Å:- Chain A: Y.22, E.235, K.239
- Ligands: SO4.4
Ligand excluded by PLIP1PE.11: 7 residues within 4Å:- Chain A: Y.22, N.23, H.27, F.208, K.239, L.240, Y.330
Ligand excluded by PLIP1PE.12: 7 residues within 4Å:- Chain A: Q.9, S.12, L.13, D.14, P.15, T.16, Y.223
Ligand excluded by PLIP1PE.20: 7 residues within 4Å:- Chain B: Y.22, N.23, H.27, F.208, K.239, Y.330
- Ligands: 1PE.21
Ligand excluded by PLIP1PE.21: 4 residues within 4Å:- Chain B: Y.22, E.235, K.239
- Ligands: 1PE.20
Ligand excluded by PLIP1PE.30: 4 residues within 4Å:- Chain C: Y.22, E.235, K.239
- Ligands: SO4.25
Ligand excluded by PLIP1PE.31: 6 residues within 4Å:- Chain C: Y.22, N.23, H.27, F.208, K.239, Y.330
Ligand excluded by PLIP1PE.32: 5 residues within 4Å:- Chain C: I.448, I.449, N.450, E.451
- Chain D: Y.418
Ligand excluded by PLIP1PE.40: 7 residues within 4Å:- Chain D: Y.22, N.23, H.27, F.208, K.239, L.240, Y.330
Ligand excluded by PLIP1PE.41: 4 residues within 4Å:- Chain D: Y.22, E.235, K.239
- Ligands: SO4.38
Ligand excluded by PLIP1PE.42: 5 residues within 4Å:- Chain D: L.433, S.436, K.437, V.443, W.444
Ligand excluded by PLIP1PE.43: 7 residues within 4Å:- Chain D: Q.9, S.12, L.13, D.14, P.15, T.16, Y.223
Ligand excluded by PLIP1PE.49: 5 residues within 4Å:- Chain E: Y.22, H.27, F.208, K.239, Y.330
Ligand excluded by PLIP1PE.50: 5 residues within 4Å:- Chain E: S.12, L.13, D.14, P.15, T.16
Ligand excluded by PLIP1PE.51: 4 residues within 4Å:- Chain E: Y.22, E.235, K.239
- Ligands: SO4.48
Ligand excluded by PLIP1PE.57: 7 residues within 4Å:- Chain F: Y.22, N.23, H.27, F.208, K.239, Y.330
- Ligands: 1PE.62
Ligand excluded by PLIP1PE.58: 5 residues within 4Å:- Chain D: S.173
- Chain F: N.368, K.370, D.462, Q.486
Ligand excluded by PLIP1PE.59: 4 residues within 4Å:- Chain A: W.444, W.445
- Chain F: L.433, W.445
Ligand excluded by PLIP1PE.62: 6 residues within 4Å:- Chain F: Y.22, N.23, E.235, K.239
- Ligands: SO4.56, 1PE.57
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.10: 21 residues within 4Å:- Chain A: K.293, D.298, K.305, G.309, S.310, M.311, L.314, F.317, D.318, D.378, E.380, G.381, L.406, T.407, G.408, L.411, A.496, F.502
- Ligands: ZN.1, CO3.2, ZN.3
10 PLIP interactions:10 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
- Water bridges: A:S.473
- pi-Cation interactions: A:K.305
- Halogen bonds: A:G.309
4TL.18: 22 residues within 4Å:- Chain B: 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, S.473, A.496, F.502
- Ligands: ZN.13, CO3.14, ZN.15
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
- pi-Cation interactions: B:K.305
- Halogen bonds: B:G.309
4TL.33: 21 residues within 4Å:- Chain C: K.293, D.298, K.305, G.309, S.310, M.311, L.314, F.317, D.318, D.378, E.380, G.381, L.406, T.407, G.408, L.411, A.496, F.502
- Ligands: ZN.22, CO3.23, ZN.24
10 PLIP interactions:10 interactions with chain C- Hydrophobic interactions: C:F.317
- Hydrogen bonds: 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
- Halogen bonds: C:G.309
4TL.44: 20 residues within 4Å:- Chain D: K.293, D.298, K.305, G.309, M.311, L.314, M.315, D.378, E.380, G.381, R.382, L.406, T.407, G.408, L.411, A.496, F.502
- Ligands: ZN.34, CO3.35, ZN.36
9 PLIP interactions:9 interactions with chain D- Hydrogen bonds: D:K.305, D:D.378, D:E.380, D:G.381, D:L.406, D:G.408
- Water bridges: D:A.409
- pi-Cation interactions: D:K.305
- Halogen bonds: D:G.309
4TL.52: 22 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, T.405, L.406, T.407, G.408, L.411, A.496, F.502
- Ligands: ZN.45, CO3.46, ZN.47
9 PLIP interactions:9 interactions with chain E- Hydrogen bonds: E:K.305, E:D.378, E:E.380, E:G.381, E:L.406, E:G.408
- Water bridges: E:A.409
- pi-Cation interactions: E:K.305
- Halogen bonds: E:G.309
4TL.60: 19 residues within 4Å:- Chain F: K.293, D.298, K.305, G.309, S.310, M.311, L.314, D.378, E.380, G.381, L.406, T.407, G.408, L.411, A.496, F.502
- Ligands: ZN.53, CO3.54, ZN.55
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
- Water bridges: F:A.409
- 2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.19: 7 residues within 4Å:- Chain A: Y.460
- Chain B: Y.163, D.168, Y.211, S.214, A.218, K.506
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:S.214
- Salt bridges: B:D.168
DMS.61: 4 residues within 4Å:- Chain F: S.5, E.6, V.7, T.16
1 PLIP interactions:1 interactions with chain F- Water bridges: F:N.231
- 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
GB
HC
ID
JE
KF
L
- 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)
- 15 x SO4: SULFATE ION(Non-functional Binders)
- 21 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)
- 2 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
GB
HC
ID
JE
KF
L