- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x 4U5: N-{(1R)-2-(hydroxyamino)-1-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-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: 4U5.1, ZN.3
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.298, A:D.318, A:D.318, A:E.380
ZN.3: 5 residues within 4Å:- Chain A: D.298, D.378, E.380
- Ligands: 4U5.1, 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, 4U5.1
ZN.11: 6 residues within 4Å:- Chain B: K.293, D.298, D.318, E.380
- Ligands: 4U5.10, ZN.12
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.298, B:D.318, B:D.318, B:E.380
ZN.12: 5 residues within 4Å:- Chain B: D.298, D.378, E.380
- Ligands: 4U5.10, 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, 4U5.10
ZN.18: 6 residues within 4Å:- Chain C: K.293, D.298, D.318, E.380
- Ligands: 4U5.17, ZN.19
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.298, C:D.318, C:D.318, C:E.380
ZN.19: 6 residues within 4Å:- Chain C: D.298, K.305, D.378, E.380
- Ligands: 4U5.17, ZN.18
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, 4U5.17
ZN.26: 7 residues within 4Å:- Chain D: K.293, D.298, D.318, E.380
- Ligands: 4U5.25, ZN.27, CO3.28
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.298, D:D.318, D:E.380
ZN.27: 6 residues within 4Å:- Chain D: D.298, K.305, D.378, E.380
- Ligands: 4U5.25, ZN.26
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, 4U5.25
ZN.34: 6 residues within 4Å:- Chain E: K.293, D.298, D.318, E.380
- Ligands: 4U5.33, ZN.35
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:D.298, E:D.318, E:D.318, E:E.380
ZN.35: 6 residues within 4Å:- Chain E: D.298, K.305, D.378, E.380
- Ligands: 4U5.33, ZN.34
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, 4U5.33
ZN.44: 6 residues within 4Å:- Chain F: D.298, K.305, D.378, E.380
- Ligands: 4U5.43, ZN.45
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, 4U5.43
ZN.45: 6 residues within 4Å:- Chain F: K.293, D.298, D.318, E.380
- Ligands: 4U5.43, ZN.44
4 PLIP interactions:4 interactions with chain F- Metal complexes: F:D.298, F:D.318, F:D.318, F:E.380
- 6 x CO3: CARBONATE ION(Non-functional Binders)
CO3.4: 8 residues within 4Å:- Chain A: K.293, A.379, E.380, G.381, R.382, L.406, T.407
- Ligands: 4U5.1
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.382, 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: 4U5.10
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.382, B:R.382, B:L.406
CO3.20: 8 residues within 4Å:- Chain C: K.293, A.379, E.380, G.381, R.382, L.406, T.407
- Ligands: 4U5.17
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:R.382, C:R.382, C:L.406
CO3.28: 9 residues within 4Å:- Chain D: K.293, D.378, A.379, E.380, G.381, R.382, L.406
- Ligands: 4U5.25, ZN.26
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:K.293, D:G.381, D:R.382, D:L.406
CO3.36: 7 residues within 4Å:- Chain E: K.293, A.379, E.380, G.381, R.382, L.406
- Ligands: 4U5.33
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:K.293, E:R.382, E:R.382, E:R.382
CO3.46: 8 residues within 4Å:- Chain F: K.293, A.379, E.380, G.381, R.382, L.406, T.407
- Ligands: 4U5.43
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:G.381, F:R.382, F:R.382, F:R.382
- 14 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 6 residues within 4Å:- Chain A: E.44, G.45, K.137, L.138, S.139
- Chain D: K.83
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain A- Salt bridges: D:K.83
- Hydrogen bonds: A:G.45, A:S.139
SO4.14: 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 B, 2 interactions with chain A- Hydrogen bonds: C:K.355, B:K.355, A:S.354, A:K.355
- Salt bridges: C:K.355, B:K.355
SO4.15: 4 residues within 4Å:- Chain A: N.457, N.464, S.468
- Chain B: R.505
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:N.464
- Salt bridges: B:R.505
SO4.21: 3 residues within 4Å:- Chain A: R.505
- Chain C: N.464, S.468
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:N.464
- Salt bridges: A:R.505
SO4.22: 5 residues within 4Å:- Chain B: E.373, N.457, N.464, S.468
- Chain C: R.505
5 PLIP interactions:4 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:E.373, B:N.464, B:S.468
- Water bridges: B:S.468
- Salt bridges: C:R.505
SO4.29: 5 residues within 4Å:- Chain D: I.20, E.21, Y.22, N.23
- Ligands: 1PE.31
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:I.20, D:Y.22, D:N.23, D:N.23
SO4.30: 4 residues within 4Å:- Chain D: N.424, N.425, T.488, A.489
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:N.425
SO4.37: 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 D, 2 interactions with chain F, 3 interactions with chain E- Hydrogen bonds: D:K.355, F:S.354, F:K.355, E:S.354, E:K.355
- Salt bridges: E:K.355
SO4.38: 2 residues within 4Å:- Chain D: N.464
- Chain E: R.505
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain E- Hydrogen bonds: D:N.464, D:N.464
- Salt bridges: E:R.505
SO4.39: 5 residues within 4Å:- Chain E: I.20, E.21, Y.22, N.23
- Ligands: 1PE.41
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:Y.22, E:N.23, E:N.23
SO4.40: 5 residues within 4Å:- Chain E: E.44, G.45, S.103, L.138, S.139
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:G.45, E:S.103, E:S.139, E:S.139
SO4.47: 3 residues within 4Å:- Chain D: R.505
- Chain F: N.464, S.468
3 PLIP interactions:2 interactions with chain F, 1 interactions with chain D- Hydrogen bonds: F:N.464, F:S.468
- Salt bridges: D:R.505
SO4.48: 3 residues within 4Å:- Chain E: N.464, S.468
- Chain F: R.505
4 PLIP interactions:1 interactions with chain F, 3 interactions with chain E- Salt bridges: F:R.505
- Hydrogen bonds: E:N.464, E:S.468
- Water bridges: E:N.464
SO4.49: 5 residues within 4Å:- Chain F: I.20, E.21, Y.22, N.23
- Ligands: 1PE.52
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)
- 13 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
1PE.7: 4 residues within 4Å:- Chain A: Y.22, H.27, K.239, Y.330
No protein-ligand interaction detected (PLIP)1PE.8: 5 residues within 4Å:- Chain A: Y.34, N.41, E.43, Y.189
- Ligands: 1PE.9
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.41
1PE.9: 4 residues within 4Å:- Chain A: G.39, N.41, N.68
- Ligands: 1PE.8
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.41
1PE.16: 4 residues within 4Å:- Chain B: Y.22, E.235, Q.238, 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, N.23, E.235, Q.238, K.239
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
No protein-ligand interaction detected (PLIP)1PE.31: 5 residues within 4Å:- Chain D: Y.22, N.23, E.235, K.239
- Ligands: SO4.29
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
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:N.23, D:H.27, D:Y.330
1PE.41: 5 residues within 4Å:- Chain E: Y.22, E.235, Q.238, K.239
- Ligands: SO4.39
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:K.239
1PE.42: 6 residues within 4Å:- Chain E: Y.22, N.23, H.27, F.208, K.239, Y.330
No protein-ligand interaction detected (PLIP)1PE.50: 6 residues within 4Å:- Chain A: A.120, Y.418
- Chain F: I.448, I.449, N.450, E.451
4 PLIP interactions:1 interactions with chain A, 3 interactions with chain F- Water bridges: A:S.118
- Hydrogen bonds: F:N.450, F:E.451, F:E.451
1PE.51: 6 residues within 4Å:- Chain F: Y.22, H.27, F.208, K.239, Y.330
- Ligands: 1PE.52
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:K.239
1PE.52: 7 residues within 4Å:- Chain F: Y.22, N.23, E.235, Q.238, K.239
- Ligands: SO4.49, 1PE.51
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:K.239
- 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 2.50 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x 4U5: N-{(1R)-2-(hydroxyamino)-1-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-2-oxoethyl}-2,2-dimethylpropanamide(Non-covalent)
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x CO3: CARBONATE ION(Non-functional Binders)
- 14 x SO4: SULFATE ION(Non-functional Binders)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 13 x 1PE: PENTAETHYLENE GLYCOL(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