- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x 4TK: N-[(1R)-1-(4-bromophenyl)-2-(hydroxyamino)-2-oxoethyl]-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: 4TK.1, ZN.3
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.298, A:D.318, A:E.380
ZN.3: 6 residues within 4Å:- Chain A: D.298, K.305, D.378, E.380
- Ligands: 4TK.1, ZN.2
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Ligand interactions- Metal complexes: A:D.298, A:D.298, A:D.378, A:D.378, 4TK.1
ZN.13: 7 residues within 4Å:- Chain B: K.293, D.298, D.318, E.380
- Ligands: 4TK.12, ZN.14, CO3.15
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.318, B:E.380, H2O.6
ZN.14: 5 residues within 4Å:- Chain B: D.298, D.378, E.380
- Ligands: 4TK.12, ZN.13
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, 4TK.12
ZN.20: 6 residues within 4Å:- Chain C: K.293, D.298, D.318, E.380
- Ligands: 4TK.19, ZN.21
3 PLIP interactions:3 interactions with chain C- Metal complexes: C:D.298, C:D.318, C:E.380
ZN.21: 6 residues within 4Å:- Chain C: D.298, K.305, D.378, E.380
- Ligands: 4TK.19, 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, 4TK.19
ZN.30: 7 residues within 4Å:- Chain D: K.293, D.298, D.318, E.380
- Ligands: 4TK.29, ZN.31, CO3.32
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.298, D:D.318, D:E.380
ZN.31: 6 residues within 4Å:- Chain D: D.298, K.305, D.378, E.380
- Ligands: 4TK.29, ZN.30
5 PLIP interactions:5 interactions with chain D- Metal complexes: D:D.298, D:D.378, D:D.378, D:E.380, D:E.380
ZN.39: 6 residues within 4Å:- Chain E: K.293, D.298, D.318, E.380
- Ligands: 4TK.38, ZN.40
3 PLIP interactions:3 interactions with chain E- Metal complexes: E:D.298, E:D.318, E:E.380
ZN.40: 6 residues within 4Å:- Chain E: D.298, K.305, D.378, E.380
- Ligands: 4TK.38, ZN.39
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, 4TK.38
ZN.44: 6 residues within 4Å:- Chain F: K.293, D.298, D.318, E.380
- Ligands: 4TK.43, ZN.45
4 PLIP interactions:3 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:D.298, F:D.318, F:E.380, H2O.25
ZN.45: 5 residues within 4Å:- Chain F: D.298, D.378, E.380
- Ligands: 4TK.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, 4TK.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: 4TK.1
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.382, A:R.382, A:L.406
CO3.15: 8 residues within 4Å:- Chain B: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TK.12, ZN.13
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.382, B:R.382, B:L.406
CO3.22: 7 residues within 4Å:- Chain C: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TK.19
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.382, C:R.382, C:L.406
CO3.32: 8 residues within 4Å:- Chain D: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TK.29, ZN.30
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:G.381, D:R.382, D:L.406
CO3.41: 7 residues within 4Å:- Chain E: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TK.38
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:G.381, E:R.382, E:R.382, E:R.382
CO3.46: 7 residues within 4Å:- Chain F: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4TK.43
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:G.381, F:R.382, F:R.382, F:R.382
- 3 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 4 residues within 4Å:- Chain A: G.309, S.310, M.311, D.313
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:G.309, A:S.310, A:S.310, A:M.311
- Water bridges: A:D.313, A:D.313
GOL.23: 5 residues within 4Å:- Chain C: I.448, I.449, N.450, E.451
- Chain D: Y.418
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:N.450, C:E.451, D:Y.418
GOL.33: 3 residues within 4Å:- Chain D: E.427, N.430, K.431
No protein-ligand interaction detected (PLIP)- 3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.6: 3 residues within 4Å:- Chain A: Y.399, K.431, D.522
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.431
- Salt bridges: A:D.522
DMS.24: 1 residues within 4Å:- Chain C: Y.244
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Y.244
- pi-Cation interactions: C:Y.244
DMS.34: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)- 10 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.7: 5 residues within 4Å:- Chain A: Y.22, N.23, H.27, K.239, Y.330
No protein-ligand interaction detected (PLIP)1PE.8: 4 residues within 4Å:- Chain A: Y.34, N.41, Y.189
- Ligands: 1PE.9
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.41
1PE.9: 5 residues within 4Å:- Chain A: Y.34, G.39, N.41, Y.189
- Ligands: 1PE.8
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.41, A:N.68, A:Y.189, A:Y.189
1PE.16: 3 residues within 4Å:- Chain B: Y.22, K.239, Y.330
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:K.239
1PE.17: 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.25: 5 residues within 4Å:- Chain C: Y.22, E.235, Q.238, K.239
- Ligands: SO4.27
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:K.239
- Hydrogen bonds: C:E.235, C:K.239
1PE.26: 6 residues within 4Å:- Chain C: Y.22, N.23, H.27, K.239, L.240, Y.330
No protein-ligand interaction detected (PLIP)1PE.35: 7 residues within 4Å:- Chain D: Y.22, N.23, H.27, F.208, K.239, L.240, Y.330
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:Y.330
1PE.42: 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:Y.330
1PE.47: 5 residues within 4Å:- Chain F: Y.22, N.23, F.208, K.239, Y.330
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:K.239
- 8 x SO4: SULFATE ION(Non-functional Binders)
SO4.10: 4 residues within 4Å:- Chain A: I.20, E.21, Y.22, N.23
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:I.20, A:Y.22, A:N.23, A:N.23
SO4.11: 5 residues within 4Å:- Chain A: E.44, G.45, L.138, S.139
- Chain D: K.83
5 PLIP interactions:1 interactions with chain D, 4 interactions with chain A- Salt bridges: D:K.83
- Hydrogen bonds: A:G.45, A:S.139, A:S.139
- Water bridges: A:S.139
SO4.18: 6 residues within 4Å:- Chain A: S.354, K.355
- Chain B: S.354, K.355
- Chain C: S.354, K.355
6 PLIP interactions:2 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: C:K.355, A:S.354, A:K.355, B:K.355
- Salt bridges: C:K.355, B:K.355
SO4.27: 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
SO4.28: 4 residues within 4Å:- Chain C: G.45, K.137, L.138, S.139
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
SO4.36: 9 residues within 4Å:- Chain A: F.75, N.80, M.81, K.83, F.84
- Chain D: Y.95, M.96, F.97, S.103
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.83
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:3 interactions with chain E, 2 interactions with chain F, 2 interactions with chain D- Hydrogen bonds: E:S.354, E:K.355, F:S.354, F:K.355, D:K.355
- Salt bridges: E:K.355, D:K.355
SO4.48: 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
- 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 2.60 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x 4TK: N-[(1R)-1-(4-bromophenyl)-2-(hydroxyamino)-2-oxoethyl]-2,2-dimethylpropanamide(Non-covalent)
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 3 x GOL: GLYCEROL(Non-functional Binders)
- 3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 10 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 8 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