- 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
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.298, A:D.318, A:E.380, H2O.4
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
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.298, B:D.318, B:E.380, H2O.13
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.19: 6 residues within 4Å:- Chain C: D.298, K.305, D.378, E.380
- Ligands: 4TM.18, ZN.20
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.18
ZN.20: 6 residues within 4Å:- Chain C: K.293, D.298, D.318, E.380
- Ligands: 4TM.18, ZN.19
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.298, C:D.318, C:E.380, H2O.22
ZN.29: 6 residues within 4Å:- Chain D: D.298, K.305, D.378, E.380
- Ligands: 4TM.28, ZN.30
5 PLIP interactions:5 interactions with chain D- Metal complexes: D:D.298, D:D.298, D:D.378, D:D.378, D:E.380
ZN.30: 6 residues within 4Å:- Chain D: K.293, D.298, D.318, E.380
- Ligands: 4TM.28, ZN.29
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:D.298, D:D.318, D:D.318, D:E.380, H2O.35
ZN.36: 6 residues within 4Å:- Chain E: K.293, D.298, D.318, E.380
- Ligands: 4TM.35, ZN.37
4 PLIP interactions:3 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:D.298, E:D.318, E:E.380, H2O.44
ZN.37: 6 residues within 4Å:- Chain E: D.298, K.305, D.378, E.380
- Ligands: 4TM.35, 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.35
ZN.44: 7 residues within 4Å:- Chain F: K.293, D.298, D.318, E.380
- Ligands: 4TM.43, ZN.45, CO3.46
4 PLIP interactions:3 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:D.298, F:D.318, F:E.380, H2O.60
ZN.45: 6 residues within 4Å:- Chain F: D.298, K.305, D.378, E.380
- Ligands: 4TM.43, ZN.44
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.43
- 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
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.293, 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
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.382, B:R.382, B:R.382
CO3.21: 7 residues within 4Å:- Chain C: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TM.18
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:A.379, C:G.381, C:R.382, C:L.406
CO3.31: 8 residues within 4Å:- Chain D: K.293, A.379, E.380, G.381, R.382, L.406, T.407
- Ligands: 4TM.28
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:R.382, D:R.382, D:L.406
CO3.38: 7 residues within 4Å:- Chain E: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TM.35
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:G.381, E:R.382, E:L.406
CO3.46: 8 residues within 4Å:- Chain F: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TM.43, ZN.44
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:R.382, F:R.382, F:L.406
- 13 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
1 PLIP interactions:1 interactions with chain A- Water bridges: A:Y.330
1PE.6: 5 residues within 4Å:- Chain A: Y.34, N.41, E.43, Y.189
- Ligands: 1PE.7
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.34, A:N.41
- Water bridges: A:Y.189
1PE.7: 3 residues within 4Å:- Chain A: N.41, N.68
- Ligands: 1PE.6
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.41
1PE.14: 3 residues within 4Å:- Chain B: Y.22, E.235, K.239
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:Y.22
- Hydrogen bonds: B:K.239
1PE.23: 5 residues within 4Å:- Chain C: Y.22, E.235, Q.238, K.239
- Ligands: SO4.25
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:K.239
- Hydrogen bonds: C:K.239
1PE.24: 6 residues within 4Å:- Chain C: Y.22, N.23, H.27, F.208, K.239, Y.330
1 PLIP interactions:1 interactions with chain C- Water bridges: C:Y.330
1PE.32: 4 residues within 4Å:- Chain D: Y.22, N.23, E.235, K.239
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:K.239
- Water bridges: D:E.235, D:K.239
1PE.33: 5 residues within 4Å:- Chain D: Y.22, H.27, F.208, K.239, Y.330
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:H.27
1PE.39: 4 residues within 4Å:- Chain E: Y.22, E.235, K.239
- Ligands: SO4.42
2 PLIP interactions:2 interactions with chain E- Hydrophobic interactions: E:K.239
- Hydrogen bonds: E:K.239
1PE.40: 5 residues within 4Å:- Chain E: Y.22, H.27, F.208, K.239, Y.330
1 PLIP interactions:1 interactions with chain E- Water bridges: E:T.334
1PE.47: 5 residues within 4Å:- Chain D: S.173
- Chain F: N.368, K.370, D.462, Q.486
4 PLIP interactions:3 interactions with chain F, 1 interactions with chain D- Hydrogen bonds: F:N.368, F:K.370, F:Q.486, D:S.173
1PE.48: 7 residues within 4Å:- Chain A: E.119, A.120, Y.418
- Chain F: I.448, I.449, N.450, E.451
7 PLIP interactions:2 interactions with chain A, 5 interactions with chain F- Hydrogen bonds: A:E.119, A:Y.418, F:N.450, F:N.450, F:E.451
- Water bridges: F:I.448, F:E.451
1PE.49: 6 residues within 4Å:- Chain F: Y.22, N.23, H.27, F.208, K.239, Y.330
No protein-ligand interaction detected (PLIP)- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 4 residues within 4Å:- Chain A: I.20, E.21, Y.22, N.23
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.22, A:N.23, A:N.23
SO4.9: 5 residues within 4Å:- Chain A: A.307, P.308, G.309, S.310, M.311
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:A.307, A:G.309, A:S.310, A:M.311
- Water bridges: A:I.312, A:I.312
SO4.15: 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
SO4.16: 5 residues within 4Å:- Chain B: A.307, P.308, G.309, S.310, M.311
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:A.307, B:G.309, B:S.310, B:M.311
- Water bridges: B:I.312
SO4.17: 4 residues within 4Å:- Chain B: I.448, I.449, N.450
- Chain E: Y.418
6 PLIP interactions:3 interactions with chain E, 3 interactions with chain B- Hydrogen bonds: E:Y.418, B:N.450, B:N.450
- Water bridges: E:E.119, E:Y.418, B:E.451
SO4.25: 5 residues within 4Å:- Chain C: I.20, E.21, Y.22, N.23
- Ligands: 1PE.23
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Y.22, C:N.23
SO4.26: 3 residues within 4Å:- Chain C: G.45, L.138, S.139
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain E- Hydrogen bonds: C:G.45, C:S.139, C:S.139
- Salt bridges: E:K.83
SO4.27: 4 residues within 4Å:- Chain C: P.308, G.309, S.310, M.311
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:G.309, C:S.310, C:M.311
- Water bridges: C:I.312
SO4.34: 6 residues within 4Å:- Chain D: S.354, K.355
- Chain E: S.354, K.355
- Chain F: S.354, K.355
5 PLIP interactions:1 interactions with chain F, 2 interactions with chain E, 2 interactions with chain D- Hydrogen bonds: F:K.355, E:K.355, D:K.355
- Salt bridges: E:K.355, D:K.355
SO4.41: 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:3 interactions with chain C, 1 interactions with chain E- Hydrogen bonds: C:N.80, E:S.103
- Water bridges: C:K.83
- Salt bridges: C:K.83
SO4.42: 5 residues within 4Å:- Chain E: I.20, E.21, Y.22, N.23
- Ligands: 1PE.39
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Y.22, E:N.23
SO4.50: 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, F:N.23
- 1 x GOL: GLYCEROL(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 2.20 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)
- 13 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 1 x GOL: GLYCEROL(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