- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.85 Å
- Oligo State
- homo-tetramer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 10 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 3 residues within 4Å:- Chain A: S.165, T.166, S.167
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:S.165, A:T.166, A:S.167, A:S.167, A:T.197, A:T.197
GOL.3: 4 residues within 4Å:- Chain A: P.138, S.139, Q.140, K.244
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.140, A:Q.140
GOL.8: 5 residues within 4Å:- Chain A: Y.132, G.134
- Chain D: A.17
- Ligands: MG.4, 8G4.9
3 PLIP interactions:3 interactions with chain A- Water bridges: A:Y.132, A:G.134, A:D.188
GOL.11: 7 residues within 4Å:- Chain A: L.295, Q.299
- Chain B: Y.266, Q.270, G.274, I.275, D.276
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:D.276, A:Q.299, A:Q.299
GOL.13: 7 residues within 4Å:- Chain A: V.263, Y.306
- Chain C: C.6, A.7, T.8
- Chain D: C.11, A.12
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.306
GOL.15: 3 residues within 4Å:- Chain E: S.165, T.166, S.167
6 PLIP interactions:6 interactions with chain E- Hydrogen bonds: E:S.165, E:T.166, E:T.166, E:S.167, E:S.167, E:T.197
GOL.16: 4 residues within 4Å:- Chain E: P.138, S.139, Q.140, K.244
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Q.140, E:Q.140
GOL.21: 5 residues within 4Å:- Chain E: Y.132, G.134
- Chain H: A.17
- Ligands: MG.17, 8G4.22
3 PLIP interactions:3 interactions with chain E- Water bridges: E:Y.132, E:G.134, E:D.188
GOL.24: 7 residues within 4Å:- Chain E: L.295, Q.299
- Chain F: Y.266, Q.270, G.274, I.275, D.276
4 PLIP interactions:2 interactions with chain F, 2 interactions with chain E- Hydrogen bonds: F:D.276, F:D.276, E:Q.299, E:Q.299
GOL.26: 7 residues within 4Å:- Chain E: V.263, Y.306
- Chain G: C.6, A.7, T.8
- Chain H: C.11, A.12
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Y.306, E:Y.306
- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.4: 5 residues within 4Å:- Chain A: D.131, D.188
- Ligands: MG.5, GOL.8, 8G4.9
5 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: A:D.131, A:D.188, H2O.1, H2O.1, 8G4.9
MG.5: 5 residues within 4Å:- Chain A: D.131, E.224, N.227
- Ligands: MG.4, 8G4.9
5 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: A:D.131, A:E.224, A:E.224, H2O.7, 8G4.9
MG.12: 2 residues within 4Å:- Chain B: D.131, D.188
1 PLIP interactions:1 interactions with chain B- Metal complexes: B:D.188
MG.17: 5 residues within 4Å:- Chain E: D.131, D.188
- Ligands: MG.18, GOL.21, 8G4.22
5 PLIP interactions:2 interactions with chain E, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: E:D.131, E:D.188, H2O.7, H2O.8, 8G4.22
MG.18: 5 residues within 4Å:- Chain E: D.131, E.224, N.227
- Ligands: MG.17, 8G4.22
5 PLIP interactions:3 interactions with chain E, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions- Metal complexes: E:D.131, E:E.224, E:E.224, H2O.14, 8G4.22
MG.25: 2 residues within 4Å:- Chain F: D.131, D.188
1 PLIP interactions:1 interactions with chain F- Metal complexes: F:D.188
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 5 residues within 4Å:- Chain A: S.335, L.336, R.339
- Chain E: K.231
- Chain H: A.17
5 PLIP interactions:2 interactions with chain E, 3 interactions with chain A- Water bridges: E:K.231, A:R.339
- Salt bridges: E:K.231, A:R.339
- Hydrogen bonds: A:L.336
SO4.7: 3 residues within 4Å:- Chain A: H.341, K.342, H.360
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.342
- Salt bridges: A:H.341, A:K.342, A:H.360
SO4.10: 5 residues within 4Å:- Chain B: K.222, R.225, S.261, P.262, V.263
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:V.263
- Salt bridges: B:K.222, B:R.225
SO4.19: 5 residues within 4Å:- Chain A: K.231
- Chain D: A.17
- Chain E: S.335, L.336, R.339
5 PLIP interactions:3 interactions with chain E, 2 interactions with chain A- Hydrogen bonds: E:L.336
- Water bridges: E:R.339, A:K.231
- Salt bridges: E:R.339, A:K.231
SO4.20: 3 residues within 4Å:- Chain E: H.341, K.342, H.360
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:K.342
- Water bridges: E:H.360
- Salt bridges: E:H.341, E:K.342, E:H.360
SO4.23: 5 residues within 4Å:- Chain F: K.222, R.225, S.261, P.262, V.263
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:V.263
- Salt bridges: F:K.222, F:R.225
- 2 x 8G4: (1S,2S,5R)-8'-[(3-chloro-4-fluorophenyl)methyl]-2'-[2-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)ethyl]-6'-hydroxy-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione(Non-covalent)
8G4.9: 12 residues within 4Å:- Chain A: D.131, D.188, G.190, P.217, Q.218, E.224
- Chain C: G.4
- Chain D: C.16, A.17
- Ligands: MG.4, MG.5, GOL.8
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:P.217, A:P.217
- Hydrogen bonds: A:D.188
- Water bridges: A:N.227
8G4.22: 12 residues within 4Å:- Chain E: D.131, D.188, G.190, P.217, Q.218, E.224
- Chain G: G.4
- Chain H: C.16, A.17
- Ligands: MG.17, MG.18, GOL.21
4 PLIP interactions:4 interactions with chain E- Hydrophobic interactions: E:P.217, E:P.217
- Water bridges: E:E.224, E:N.227
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Schreier, J.D. et al., Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV. Bioorg. Med. Chem. Lett. (2017)
- Release Date
- 2017-03-29
- Peptides
- INTEGRASE: ABEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.85 Å
- Oligo State
- homo-tetramer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 10 x GOL: GLYCEROL(Non-functional Binders)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- 2 x 8G4: (1S,2S,5R)-8'-[(3-chloro-4-fluorophenyl)methyl]-2'-[2-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)ethyl]-6'-hydroxy-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Schreier, J.D. et al., Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV. Bioorg. Med. Chem. Lett. (2017)
- Release Date
- 2017-03-29
- Peptides
- INTEGRASE: ABEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
B