- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.62 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 2 x R7K: ~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-5-(hydroxymethyl)-1,4-bis(oxidanyl)-2-oxidanylidene-1,8-naphthyridine-3-carboxamide(Non-covalent)
R7K.3: 12 residues within 4Å:- Chain A: D.131, D.188, P.217, Q.218, E.224
- Chain C: G.4
- Chain D: C.16, A.17
- Ligands: MG.1, MG.2, SO4.8, MES.17
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:P.217, A:P.217
- Water bridges: A:Y.132, A:N.227, A:R.332, A:R.332
- Halogen bonds: A:E.224
R7K.25: 12 residues within 4Å:- Chain E: D.131, D.188, P.217, Q.218, E.224
- Chain G: G.4
- Chain H: C.16, A.17
- Ligands: MG.23, MG.24, SO4.30, MES.39
7 PLIP interactions:7 interactions with chain E- Hydrophobic interactions: E:P.217, E:P.217
- Water bridges: E:Y.132, E:N.227, E:R.332, E:R.332
- Halogen bonds: E:E.224
- 2 x ZN: ZINC ION(Non-covalent)
ZN.4: 4 residues within 4Å:- Chain A: H.65, H.69, C.99, C.102
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:H.65, A:H.69, A:C.99, A:C.102
ZN.26: 4 residues within 4Å:- Chain E: H.65, H.69, C.99, C.102
4 PLIP interactions:4 interactions with chain E- Metal complexes: E:H.65, E:H.69, E:C.99, E:C.102
- 22 x SO4: SULFATE ION(Non-functional Binders)
SO4.5: 4 residues within 4Å:- Chain A: S.335, L.336, R.339
- Chain E: K.231
Ligand excluded by PLIPSO4.6: 3 residues within 4Å:- Chain A: P.118, D.119
- Chain C: T.3
Ligand excluded by PLIPSO4.7: 4 residues within 4Å:- Chain A: P.138, S.139, Q.140, K.244
Ligand excluded by PLIPSO4.8: 4 residues within 4Å:- Chain A: G.190, A.191
- Ligands: R7K.3, MES.17
Ligand excluded by PLIPSO4.9: 3 residues within 4Å:- Chain A: H.341, K.342, H.360
Ligand excluded by PLIPSO4.10: 3 residues within 4Å:- Chain A: G.21, H.22, Y.23
Ligand excluded by PLIPSO4.11: 7 residues within 4Å:- Chain A: L.76, A.80, W.84, M.88, R.89
- Chain H: A.7, T.8
Ligand excluded by PLIPSO4.12: 6 residues within 4Å:- Chain A: R.337, R.339
- Chain E: K.231, R.232, T.235
- Chain H: C.16
Ligand excluded by PLIPSO4.18: 5 residues within 4Å:- Chain B: K.222, R.225, S.261, P.262, V.263
Ligand excluded by PLIPSO4.19: 2 residues within 4Å:- Chain B: S.220, G.221
Ligand excluded by PLIPSO4.22: 2 residues within 4Å:- Chain D: G.4, A.5
Ligand excluded by PLIPSO4.27: 4 residues within 4Å:- Chain A: K.231
- Chain E: S.335, L.336, R.339
Ligand excluded by PLIPSO4.28: 3 residues within 4Å:- Chain E: P.118, D.119
- Chain G: T.3
Ligand excluded by PLIPSO4.29: 4 residues within 4Å:- Chain E: P.138, S.139, Q.140, K.244
Ligand excluded by PLIPSO4.30: 4 residues within 4Å:- Chain E: G.190, A.191
- Ligands: R7K.25, MES.39
Ligand excluded by PLIPSO4.31: 3 residues within 4Å:- Chain E: H.341, K.342, H.360
Ligand excluded by PLIPSO4.32: 3 residues within 4Å:- Chain E: G.21, H.22, Y.23
Ligand excluded by PLIPSO4.33: 7 residues within 4Å:- Chain D: A.7, T.8
- Chain E: L.76, A.80, W.84, M.88, R.89
Ligand excluded by PLIPSO4.34: 6 residues within 4Å:- Chain A: K.231, R.232, T.235
- Chain D: C.16
- Chain E: R.337, R.339
Ligand excluded by PLIPSO4.40: 5 residues within 4Å:- Chain F: K.222, R.225, S.261, P.262, V.263
Ligand excluded by PLIPSO4.41: 2 residues within 4Å:- Chain F: S.220, G.221
Ligand excluded by PLIPSO4.44: 2 residues within 4Å:- Chain H: G.4, A.5
Ligand excluded by PLIP- 12 x GOL: GLYCEROL(Non-functional Binders)
GOL.13: 3 residues within 4Å:- Chain A: S.165, T.166, S.167
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.167, A:S.167
GOL.14: 5 residues within 4Å:- Chain A: R.117, Y.306, P.308
- Chain C: C.6
- Ligands: GOL.21
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.117, A:R.117, A:Y.306, A:Y.306
GOL.15: 5 residues within 4Å:- Chain A: Q.63, L.82, Y.83
- Chain E: P.280, F.281
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain E- Hydrogen bonds: A:Q.63, A:Y.83, E:F.281
GOL.16: 6 residues within 4Å:- Chain A: K.342, L.358, D.359, H.360, L.361, G.362
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.342, A:L.361
- Water bridges: A:T.345
GOL.20: 7 residues within 4Å:- Chain A: L.295, Q.299
- Chain B: Y.266, Q.270, G.274, I.275, D.276
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:I.275
GOL.21: 7 residues within 4Å:- Chain A: V.263
- Chain C: C.6, A.7, T.8
- Chain D: C.11, A.12
- Ligands: GOL.14
2 PLIP interactions:2 interactions with chain A- Water bridges: A:V.263, A:Y.306
GOL.35: 3 residues within 4Å:- Chain E: S.165, T.166, S.167
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:S.167, E:S.167
GOL.36: 5 residues within 4Å:- Chain E: R.117, Y.306, P.308
- Chain G: C.6
- Ligands: GOL.43
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:R.117, E:R.117, E:Y.306
GOL.37: 5 residues within 4Å:- Chain A: P.280, F.281
- Chain E: Q.63, L.82, Y.83
4 PLIP interactions:3 interactions with chain E, 1 interactions with chain A- Hydrogen bonds: E:Q.63, E:Y.83, E:Y.83, A:F.281
GOL.38: 6 residues within 4Å:- Chain E: K.342, L.358, D.359, H.360, L.361, G.362
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:K.342, E:L.361
- Water bridges: E:T.345
GOL.42: 7 residues within 4Å:- Chain E: L.295, Q.299
- Chain F: Y.266, Q.270, G.274, I.275, D.276
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:I.275
GOL.43: 7 residues within 4Å:- Chain E: V.263
- Chain G: C.6, A.7, T.8
- Chain H: C.11, A.12
- Ligands: GOL.36
2 PLIP interactions:2 interactions with chain E- Water bridges: E:V.263, E:Y.306
- 2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
MES.17: 8 residues within 4Å:- Chain A: D.188, Q.189, G.190, P.214, Y.215, R.332
- Ligands: R7K.3, SO4.8
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.39: 8 residues within 4Å:- Chain E: D.188, Q.189, G.190, P.214, Y.215, R.332
- Ligands: R7K.25, SO4.30
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:Q.189, E:Y.215
- Water bridges: E:H.216, E:H.216
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Smith, S.J. et al., HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. Acs Infect Dis. (2021)
- Release Date
- 2021-03-24
- Peptides
- Integrase: ABEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.62 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 2 x R7K: ~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-5-(hydroxymethyl)-1,4-bis(oxidanyl)-2-oxidanylidene-1,8-naphthyridine-3-carboxamide(Non-covalent)
- 2 x ZN: ZINC ION(Non-covalent)
- 22 x SO4: SULFATE ION(Non-functional Binders)
- 12 x GOL: GLYCEROL(Non-functional Binders)
- 2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Smith, S.J. et al., HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. Acs Infect Dis. (2021)
- Release Date
- 2021-03-24
- Peptides
- Integrase: ABEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BE
AF
B