- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x 4TM: N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(thiophen-3-yl)phenyl]ethyl}-2,2-dimethylpropanamide(Non-covalent)
- 12 x ZN: ZINC ION(Non-covalent)
ZN.2: 6 residues within 4Å:- Chain A: K.293, D.298, D.318, E.380
- Ligands: 4TM.1, ZN.3
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.298, A:D.318, A:D.318, A:E.380, H2O.3
ZN.3: 6 residues within 4Å:- Chain A: D.298, K.305, D.378, E.380
- Ligands: 4TM.1, ZN.2
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Ligand interactions- Metal complexes: A:D.298, A:D.378, A:D.378, A:E.380, 4TM.1
ZN.11: 6 residues within 4Å:- Chain B: K.293, D.298, D.318, E.380
- Ligands: 4TM.10, ZN.12
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.298, B:D.318, B:D.318, B:E.380, H2O.15
ZN.12: 5 residues within 4Å:- Chain B: D.298, D.378, E.380
- Ligands: 4TM.10, ZN.11
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Ligand interactions- Metal complexes: B:D.298, B:D.378, B:D.378, B:E.380, 4TM.10
ZN.21: 6 residues within 4Å:- Chain C: D.298, K.305, D.378, E.380
- Ligands: 4TM.20, ZN.22
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Ligand interactions- Metal complexes: C:D.298, C:D.378, C:D.378, C:E.380, 4TM.20
ZN.22: 6 residues within 4Å:- Chain C: K.293, D.298, D.318, E.380
- Ligands: 4TM.20, ZN.21
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.298, C:D.318, C:D.318, C:E.380, H2O.22
ZN.28: 6 residues within 4Å:- Chain D: D.298, K.305, D.378, E.380
- Ligands: 4TM.27, ZN.29
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Ligand interactions- Metal complexes: D:D.298, D:D.378, D:D.378, D:E.380, 4TM.27
ZN.29: 6 residues within 4Å:- Chain D: K.293, D.298, D.318, E.380
- Ligands: 4TM.27, ZN.28
4 PLIP interactions:3 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.298, D:D.318, D:E.380, H2O.33
ZN.35: 6 residues within 4Å:- Chain E: D.298, K.305, D.378, E.380
- Ligands: 4TM.34, ZN.36
5 PLIP interactions:4 interactions with chain E, 1 Ligand-Ligand interactions- Metal complexes: E:D.298, E:D.378, E:D.378, E:E.380, 4TM.34
ZN.36: 6 residues within 4Å:- Chain E: K.293, D.298, D.318, E.380
- Ligands: 4TM.34, ZN.35
5 PLIP interactions:4 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:D.298, E:D.318, E:D.318, E:E.380, H2O.45
ZN.42: 6 residues within 4Å:- Chain F: K.293, D.298, D.318, E.380
- Ligands: 4TM.41, ZN.43
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.57
ZN.43: 5 residues within 4Å:- Chain F: D.298, D.378, E.380
- Ligands: 4TM.41, ZN.42
5 PLIP interactions:4 interactions with chain F, 1 Ligand-Ligand interactions- Metal complexes: F:D.298, F:D.378, F:D.378, F:E.380, 4TM.41
- 6 x CO3: CARBONATE ION(Non-functional Binders)
CO3.4: 7 residues within 4Å:- Chain A: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TM.1
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
CO3.13: 7 residues within 4Å:- Chain B: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TM.10
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: 4TM.20
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:G.381, C:R.382, C:L.406
CO3.30: 6 residues within 4Å:- Chain D: K.293, A.379, G.381, R.382, L.406
- Ligands: 4TM.27
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:R.382, D:R.382, D:R.382
CO3.37: 7 residues within 4Å:- Chain E: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TM.34
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:R.382, E:R.382, E:L.406
CO3.44: 7 residues within 4Å:- Chain F: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TM.41
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:R.382, F:R.382, F:L.406
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 11 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.6: 5 residues within 4Å:- Chain A: Y.22, N.23, H.27, K.239, Y.330
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.239
1PE.7: 5 residues within 4Å:- Chain A: Y.22, N.23, E.235, K.239
- Ligands: SO4.8
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:K.239
1PE.14: 6 residues within 4Å:- Chain B: Y.22, H.27, F.208, L.240, Y.330
- Ligands: 1PE.15
1 PLIP interactions:1 interactions with chain B- Water bridges: B:Y.330
1PE.15: 4 residues within 4Å:- Chain B: Y.22, E.235, K.239
- Ligands: 1PE.14
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:K.239
1PE.24: 6 residues within 4Å:- Chain C: Y.22, E.235, Q.238, K.239
- Ligands: 1PE.25, SO4.26
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:Q.238, C:K.239
- Hydrogen bonds: C:K.239
1PE.25: 6 residues within 4Å:- Chain C: Y.22, N.23, H.27, L.240, Y.330
- Ligands: 1PE.24
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Y.330
- Water bridges: C:T.334
1PE.31: 4 residues within 4Å:- Chain D: Y.22, E.235, Q.238, K.239
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:K.239
1PE.32: 6 residues within 4Å:- Chain D: Y.22, N.23, H.27, F.208, K.239, Y.330
No protein-ligand interaction detected (PLIP)1PE.38: 4 residues within 4Å:- Chain E: Y.22, E.235, K.239
- Ligands: 1PE.39
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:K.239
- Hydrogen bonds: E:K.239
1PE.39: 7 residues within 4Å:- Chain E: Y.22, N.23, H.27, F.208, K.239, Y.330
- Ligands: 1PE.38
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:K.239
1PE.45: 5 residues within 4Å:- Chain F: Y.22, N.23, H.27, K.239, Y.330
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:N.23, F:K.239
- 11 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 5 residues within 4Å:- Chain A: I.20, E.21, Y.22, N.23
- Ligands: 1PE.7
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.22, A:N.23, A:N.23
SO4.9: 4 residues within 4Å:- Chain A: P.308, G.309, S.310, M.311
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.309, A:M.311
- Water bridges: A:I.312
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, 3 interactions with chain C, 1 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, C:K.355
SO4.17: 5 residues within 4Å:- Chain B: S.5, E.6, V.7, T.16, N.231
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.5, B:V.7, B:T.16, B:N.231
SO4.18: 5 residues within 4Å:- Chain B: A.307, G.309, S.310, M.311, D.313
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:G.309, B:S.310, B:M.311, B:D.313
SO4.19: 4 residues within 4Å:- Chain B: I.448, I.449, N.450
- Chain E: Y.418
4 PLIP interactions:2 interactions with chain B, 2 interactions with chain E- Hydrogen bonds: B:N.450, E:Y.418
- Water bridges: B:E.451, E:E.119
SO4.26: 5 residues within 4Å:- Chain C: I.20, E.21, Y.22, N.23
- Ligands: 1PE.24
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:Y.22, C:N.23, C:N.23, C:N.23
SO4.33: 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:1 interactions with chain E, 3 interactions with chain D, 2 interactions with chain F- Hydrogen bonds: E:K.355, D:K.355, F:K.355
- Water bridges: D:K.355
- Salt bridges: D:K.355, F:K.355
SO4.40: 3 residues within 4Å:- Chain E: G.309, S.310, M.311
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:G.309, E:M.311
- Water bridges: E:A.307, E:I.312
SO4.46: 4 residues within 4Å:- Chain A: Y.418
- Chain F: I.448, I.449, N.450
7 PLIP interactions:4 interactions with chain F, 3 interactions with chain A- Hydrogen bonds: F:I.448, F:N.450, F:N.450, A:Y.418, A:Y.418
- Water bridges: F:E.451, A:S.118
SO4.47: 4 residues within 4Å:- Chain F: I.20, E.21, Y.22, N.23
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:Y.22, F:N.23
- Water bridges: F:I.20
- 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 2.20 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x 4TM: N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(thiophen-3-yl)phenyl]ethyl}-2,2-dimethylpropanamide(Non-covalent)
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 11 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 11 x SO4: SULFATE ION(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