- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.55 Å
- Oligo State
- homo-tetramer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 4 residues within 4Å:- Chain A: D.131, D.188
- Ligands: MG.3, VHT.17
4 PLIP interactions:2 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.131, A:D.188, H2O.2, H2O.3
MG.3: 5 residues within 4Å:- Chain A: D.131, E.224, N.227
- Ligands: MG.2, VHT.17
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.131, A:E.224, A:E.224, H2O.9
MG.20: 3 residues within 4Å:- Chain B: D.131, D.188, F.193
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.131, B:D.188, B:D.188
MG.27: 4 residues within 4Å:- Chain E: D.131, D.188
- Ligands: MG.28, VHT.42
4 PLIP interactions:2 interactions with chain E, 2 Ligand-Water interactions- Metal complexes: E:D.131, E:D.188, H2O.11, H2O.12
MG.28: 5 residues within 4Å:- Chain E: D.131, E.224, N.227
- Ligands: MG.27, VHT.42
4 PLIP interactions:3 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:D.131, E:E.224, E:E.224, H2O.18
MG.45: 3 residues within 4Å:- Chain F: D.131, D.188, F.193
3 PLIP interactions:3 interactions with chain F- Metal complexes: F:D.131, F:D.188, F:D.188
- 10 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 4 residues within 4Å:- Chain A: P.138, S.139, Q.140, K.244
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:S.139, A:Q.140, A:Q.140
- Water bridges: A:G.141
- Salt bridges: A:K.244
SO4.5: 3 residues within 4Å:- Chain A: H.341, K.342, H.360
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.342
- Salt bridges: A:H.341, A:H.360
SO4.6: 5 residues within 4Å:- Chain A: G.190, A.191
- Chain D: A.17
- Ligands: VHT.17, MES.18
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:A.191
- Water bridges: A:A.192
SO4.7: 5 residues within 4Å:- Chain A: A.334, S.335, L.336, R.339
- Chain E: K.231
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain E- Hydrogen bonds: A:A.334, A:L.336
- Salt bridges: A:R.339, E:K.231
SO4.21: 5 residues within 4Å:- Chain B: K.222, R.225, S.261, P.262, V.263
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.261, B:V.263
- Salt bridges: B:K.222, B:R.225
SO4.29: 4 residues within 4Å:- Chain E: P.138, S.139, Q.140, K.244
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:S.139, E:Q.140, E:Q.140
- Water bridges: E:G.141
- Salt bridges: E:K.244
SO4.30: 3 residues within 4Å:- Chain E: H.341, K.342, H.360
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:K.342
- Salt bridges: E:H.341, E:H.360
SO4.31: 5 residues within 4Å:- Chain E: G.190, A.191
- Chain H: A.17
- Ligands: VHT.42, MES.43
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:A.191
- Water bridges: E:A.192
SO4.32: 5 residues within 4Å:- Chain A: K.231
- Chain E: A.334, S.335, L.336, R.339
4 PLIP interactions:3 interactions with chain E, 1 interactions with chain A- Hydrogen bonds: E:A.334, E:L.336
- Salt bridges: E:R.339, A:K.231
SO4.46: 5 residues within 4Å:- Chain F: K.222, R.225, S.261, P.262, V.263
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:S.261, F:V.263
- Salt bridges: F:K.222, F:R.225
- 24 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 3 residues within 4Å:- Chain A: S.165, T.166, S.167
Ligand excluded by PLIPGOL.9: 5 residues within 4Å:- Chain A: R.117, Y.306, P.308
- Chain C: C.6
- Ligands: GOL.24
Ligand excluded by PLIPGOL.10: 5 residues within 4Å:- Chain A: Q.63, L.82, Y.83
- Chain E: P.280, F.281
Ligand excluded by PLIPGOL.11: 3 residues within 4Å:- Chain A: P.118, D.119
- Chain C: T.3
Ligand excluded by PLIPGOL.12: 6 residues within 4Å:- Chain A: S.228, T.235
- Chain D: A.15, C.16
- Chain E: R.337, R.339
Ligand excluded by PLIPGOL.13: 7 residues within 4Å:- Chain A: Y.215, P.217, Q.218, R.329, D.370, N.371
- Ligands: VHT.17
Ligand excluded by PLIPGOL.14: 3 residues within 4Å:- Chain A: H.22, Y.23, K.29
Ligand excluded by PLIPGOL.15: 5 residues within 4Å:- Chain A: K.342, D.359, H.360, L.361, G.362
Ligand excluded by PLIPGOL.16: 7 residues within 4Å:- Chain A: L.295, Q.299
- Chain B: Y.266, Q.270, G.274, I.275, D.276
Ligand excluded by PLIPGOL.22: 1 residues within 4Å:- Chain B: G.221
Ligand excluded by PLIPGOL.24: 8 residues within 4Å:- Chain A: V.263, Y.306
- Chain C: C.6, A.7, T.8
- Chain D: C.11, A.12
- Ligands: GOL.9
Ligand excluded by PLIPGOL.25: 2 residues within 4Å:- Chain C: A.19
- Chain D: G.2
Ligand excluded by PLIPGOL.33: 3 residues within 4Å:- Chain E: S.165, T.166, S.167
Ligand excluded by PLIPGOL.34: 5 residues within 4Å:- Chain E: R.117, Y.306, P.308
- Chain G: C.6
- Ligands: GOL.49
Ligand excluded by PLIPGOL.35: 5 residues within 4Å:- Chain A: P.280, F.281
- Chain E: Q.63, L.82, Y.83
Ligand excluded by PLIPGOL.36: 3 residues within 4Å:- Chain E: P.118, D.119
- Chain G: T.3
Ligand excluded by PLIPGOL.37: 6 residues within 4Å:- Chain A: R.337, R.339
- Chain E: S.228, T.235
- Chain H: A.15, C.16
Ligand excluded by PLIPGOL.38: 7 residues within 4Å:- Chain E: Y.215, P.217, Q.218, R.329, D.370, N.371
- Ligands: VHT.42
Ligand excluded by PLIPGOL.39: 3 residues within 4Å:- Chain E: H.22, Y.23, K.29
Ligand excluded by PLIPGOL.40: 5 residues within 4Å:- Chain E: K.342, D.359, H.360, L.361, G.362
Ligand excluded by PLIPGOL.41: 7 residues within 4Å:- Chain E: L.295, Q.299
- Chain F: Y.266, Q.270, G.274, I.275, D.276
Ligand excluded by PLIPGOL.47: 1 residues within 4Å:- Chain F: G.221
Ligand excluded by PLIPGOL.49: 8 residues within 4Å:- Chain E: V.263, Y.306
- Chain G: C.6, A.7, T.8
- Chain H: C.11, A.12
- Ligands: GOL.34
Ligand excluded by PLIPGOL.50: 2 residues within 4Å:- Chain G: A.19
- Chain H: G.2
Ligand excluded by PLIP- 2 x VHT: methyl 2-[[3-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridin-4-yl]amino]ethanoate(Non-covalent)
VHT.17: 14 residues within 4Å:- Chain A: D.131, D.188, Y.215, P.217, Q.218, E.224
- Chain C: G.4
- Chain D: C.16, A.17
- Ligands: MG.2, MG.3, SO4.6, GOL.13, MES.18
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:P.217
- Water bridges: A:Y.132, A:N.227
VHT.42: 14 residues within 4Å:- Chain E: D.131, D.188, Y.215, P.217, Q.218, E.224
- Chain G: G.4
- Chain H: C.16, A.17
- Ligands: MG.27, MG.28, SO4.31, GOL.38, MES.43
4 PLIP interactions:4 interactions with chain E- Hydrophobic interactions: E:P.217
- Hydrogen bonds: E:D.188
- Water bridges: E:Y.132, E:N.227
- 2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
MES.18: 8 residues within 4Å:- Chain A: D.188, Q.189, G.190, T.213, P.214, Y.215
- Ligands: SO4.6, VHT.17
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:Q.189, A:Y.215
- Water bridges: A:H.216, A:H.216
MES.43: 8 residues within 4Å:- Chain E: D.188, Q.189, G.190, T.213, P.214, Y.215
- Ligands: SO4.31, VHT.42
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:Q.189, E:Y.215
- Water bridges: E:H.216, E:H.216
- 4 x HEZ: HEXANE-1,6-DIOL(Non-covalent)
HEZ.19: 6 residues within 4Å:- Chain A: Y.260, K.265, Y.266, Q.270, G.274, N.283
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:Y.260, A:Y.266, A:Y.266
- Hydrogen bonds: A:G.274
HEZ.23: 6 residues within 4Å:- Chain A: S.178
- Chain B: L.158, Y.159, Y.246, P.250, Q.253
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:L.158, B:Y.246, B:Q.253
HEZ.44: 6 residues within 4Å:- Chain E: Y.260, K.265, Y.266, Q.270, G.274, N.283
4 PLIP interactions:4 interactions with chain E- Hydrophobic interactions: E:Y.260, E:Y.266, E:Y.266
- Hydrogen bonds: E:G.274
HEZ.48: 6 residues within 4Å:- Chain E: S.178
- Chain F: L.158, Y.159, Y.246, P.250, Q.253
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:L.158, F:Y.246, F:Q.253
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhao, X.Z. et al., Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors. J. Med. Chem. (2017)
- Release Date
- 2017-08-02
- Peptides
- integrase: ABEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.55 Å
- Oligo State
- homo-tetramer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 10 x SO4: SULFATE ION(Non-functional Binders)
- 24 x GOL: GLYCEROL(Non-functional Binders)
- 2 x VHT: methyl 2-[[3-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridin-4-yl]amino]ethanoate(Non-covalent)
- 2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 4 x HEZ: HEXANE-1,6-DIOL(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhao, X.Z. et al., Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors. J. Med. Chem. (2017)
- Release Date
- 2017-08-02
- Peptides
- integrase: ABEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
B