SMTL ID : 7adv.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ447 (compound 6v)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.2, R7N.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.2, H2O.2 MG.2: 6 residues within 4Å: Chain A: D.131, E.224, N.227 Chain D: A.17 Ligands: MG.1, R7N.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:E.224, A:E.224, H2O.6 MG.23: 2 residues within 4Å: Chain B: D.131, D.188 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.131, B:D.188, B:D.188 MG.29: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.30, R7N.32 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.8, H2O.8 MG.30: 6 residues within 4Å: Chain E: D.131, E.224, N.227 Chain H: A.17 Ligands: MG.29, R7N.32 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.12 MG.51: 2 residues within 4Å: Chain F: D.131, D.188 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.131, F:D.188, F:D.188

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.31: 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

2 x R7N: 4-azanyl-~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-6-[2-(2-morpholin-4-ylethylsulfonyl)ethyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridine-3-carboxamide(Non-covalent)

R7N.4: 18 residues within 4Å: Chain A: D.131, D.188, Q.189, G.190, P.214, Y.215, P.217, Q.218, E.224, R.332, R.365 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.1, MG.2, SO4.15, SO4.16 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.217, A:P.217 Hydrogen bonds: A:R.365, A:R.365 Water bridges: A:D.131, A:Y.132, A:E.224, A:E.224, A:N.227 R7N.32: 18 residues within 4Å: Chain E: D.131, D.188, Q.189, G.190, P.214, Y.215, P.217, Q.218, E.224, R.332, R.365 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.29, MG.30, SO4.43, SO4.44 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:P.217, E:P.217 Hydrogen bonds: E:R.365, E:R.365 Water bridges: E:Y.132, E:N.227

34 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain A: S.335, L.336, R.339 Chain E: K.231 Chain H: C.16 Ligands: GOL.20 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: P.118, D.119 Chain C: T.3 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: P.138, S.139, Q.140, K.244 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: T.161, K.162, A.163, A.168 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: R.117, Y.306, P.308 Chain C: C.6 Ligands: GOL.27 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: H.341, K.342, H.360 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: L.76, A.80, W.84, M.88 Chain H: T.8 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: S.309, T.310 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: Y.306, H.307, P.308, S.309 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: K.342, D.359, H.360, G.362 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: Y.215, R.332 Ligands: R7N.4 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain A: G.190, A.191 Chain D: A.17 Ligands: R7N.4 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain A: H.208 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain A: Y.266, Q.270, G.274, I.275, N.283, T.286, I.301 Ligand excluded by PLIP SO4.24: 1 residues within 4Å: Chain B: T.213 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain B: K.222, R.225, S.261, P.262, V.263 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain D: G.4, A.5 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain A: K.231 Chain D: C.16 Chain E: S.335, L.336, R.339 Ligands: GOL.48 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain E: P.118, D.119 Chain G: T.3 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain E: P.138, S.139, Q.140, K.244 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain E: T.161, K.162, A.163, A.168 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain E: R.117, Y.306, P.308 Chain G: C.6 Ligands: GOL.55 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain E: H.341, K.342, H.360 Ligand excluded by PLIP SO4.39: 5 residues within 4Å: Chain D: T.8 Chain E: L.76, A.80, W.84, M.88 Ligand excluded by PLIP SO4.40: 2 residues within 4Å: Chain E: S.309, T.310 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain E: Y.306, H.307, P.308, S.309 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain E: K.342, D.359, H.360, G.362 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain E: Y.215, R.332 Ligands: R7N.32 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain E: G.190, A.191 Chain H: A.17 Ligands: R7N.32 Ligand excluded by PLIP SO4.45: 1 residues within 4Å: Chain E: H.208 Ligand excluded by PLIP SO4.46: 7 residues within 4Å: Chain E: Y.266, Q.270, G.274, I.275, N.283, T.286, I.301 Ligand excluded by PLIP SO4.52: 1 residues within 4Å: Chain F: T.213 Ligand excluded by PLIP SO4.53: 5 residues within 4Å: Chain F: K.222, R.225, S.261, P.262, V.263 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain H: G.4, A.5 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 5 residues within 4Å: Chain A: Q.63, L.82, Y.83 Chain E: P.280, F.281 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:Q.63, E:F.281 GOL.20: 6 residues within 4Å: Chain A: R.339 Chain E: S.228, T.235 Chain H: A.15, C.16 Ligands: SO4.5 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.228 Water bridges: A:T.105 GOL.21: 3 residues within 4Å: Chain A: S.165, T.166, S.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.166, A:T.166, A:S.167 GOL.22: 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:D.276 GOL.26: 2 residues within 4Å: Chain B: G.221, R.225 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.221, B:R.225, B:R.225 GOL.27: 7 residues within 4Å: Chain A: V.263 Chain C: C.6, A.7, T.8 Chain D: C.11, A.12 Ligands: SO4.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.263 GOL.47: 5 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, L.82, Y.83 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:F.281, E:Q.63, E:Y.83 GOL.48: 6 residues within 4Å: Chain A: S.228, T.235 Chain D: A.15, C.16 Chain E: R.339 Ligands: SO4.33 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Water bridges: E:T.105 Hydrogen bonds: A:S.228, A:T.235 GOL.49: 3 residues within 4Å: Chain E: S.165, T.166, S.167 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.166, E:S.167 GOL.50: 7 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, I.275, D.276 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.276, F:D.276 GOL.54: 2 residues within 4Å: Chain F: G.221, R.225 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.221, F:R.225, F:R.225 GOL.55: 7 residues within 4Å: Chain E: V.263 Chain G: C.6, A.7, T.8 Chain H: C.11, A.12 Ligands: SO4.37 1 PLIP interactions: 1 interactions with chain E Water bridges: E:V.263

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
A

B
B

E
A

F
B

Integrase

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