SMTL ID : 5no1.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ407 (compound 5g)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.131, E.224, N.227 Ligands: MG.2, XZ4.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:E.224, A:E.224, H2O.4 MG.2: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.1, XZ4.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.2 MG.17: 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.22: 5 residues within 4Å: Chain E: D.131, E.224, N.227 Ligands: MG.23, XZ4.24 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.9 MG.23: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.22, XZ4.24 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.5, H2O.6 MG.38: 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 XZ4: methyl 2-[[3-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-7-methoxy-1-oxidanyl-2-oxidanylidene-1,8-naphthyridin-4-yl]amino]ethanoate(Non-covalent)

XZ4.3: 15 residues within 4Å: Chain A: D.131, Y.132, D.188, G.190, Y.215, P.217, Q.218, E.224 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.1, MG.2, SO4.8, MES.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.217, A:E.224 Water bridges: A:Y.132, A:Y.132, A:N.227 XZ4.24: 15 residues within 4Å: Chain E: D.131, Y.132, D.188, G.190, Y.215, P.217, Q.218, E.224 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.22, MG.23, SO4.29, MES.36 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:P.217, E:E.224 Hydrogen bonds: E:E.224 Water bridges: E:Y.132, E:Y.132, E:D.188, E:N.227

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.25: 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

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

SO4.5: 5 residues within 4Å: Chain A: R.117, Y.306, P.308 Chain C: C.6 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: 3 residues within 4Å: Chain A: S.139, Q.140, K.244 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: D.188, Q.189, G.190, P.214, Y.215 Ligands: XZ4.3, MES.15 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: K.231 Chain E: S.335, L.336, R.339 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: H.341, K.342, H.360 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain B: K.222, R.225, S.261, P.262, V.263 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain A: K.231, R.232, T.235 Chain D: A.15, C.16 Chain E: R.339 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain E: R.117, Y.306, P.308 Chain G: C.6 Ligands: GOL.41 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain E: P.118, D.119 Chain G: T.3 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain E: S.139, Q.140, K.244 Ligand excluded by PLIP SO4.29: 7 residues within 4Å: Chain E: D.188, Q.189, G.190, P.214, Y.215 Ligands: XZ4.24, MES.36 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain A: S.335, L.336, R.339 Chain E: K.231 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain E: H.341, K.342, H.360 Ligand excluded by PLIP SO4.39: 5 residues within 4Å: Chain F: K.222, R.225, S.261, P.262, V.263 Ligand excluded by PLIP SO4.42: 6 residues within 4Å: Chain A: R.339 Chain E: K.231, R.232, T.235 Chain H: A.15, C.16 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 5 residues within 4Å: Chain A: Q.63, L.82, Y.83 Chain E: P.280, F.281 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:F.281, A:Q.63, A:Y.83 GOL.12: 3 residues within 4Å: Chain A: S.165, T.166, S.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.166, A:T.166, A:S.167, A:S.167 GOL.13: 7 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, I.275, D.276 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.266, B:G.274, B:D.276, B:D.276 GOL.14: 4 residues within 4Å: Chain A: G.21, H.22, Y.23, K.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.29, A:K.29 GOL.19: 3 residues within 4Å: Chain B: S.220, G.221, R.225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.221, B:R.225 GOL.20: 7 residues within 4Å: Chain A: V.263 Chain C: C.6, A.7, T.8 Chain D: C.11, A.12 Ligands: SO4.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.263 GOL.32: 5 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, L.82, Y.83 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:F.281, E:Q.63, E:Y.83, E:Y.83 GOL.33: 3 residues within 4Å: Chain E: S.165, T.166, S.167 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.166, E:S.167, E:S.167 GOL.34: 7 residues within 4Å: Chain E: L.295, Q.299 Chain F: Y.266, Q.270, G.274, I.275, D.276 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Y.266, F:G.274, F:D.276 GOL.35: 4 residues within 4Å: Chain E: G.21, H.22, Y.23, K.29 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.29, E:K.29 GOL.40: 3 residues within 4Å: Chain F: S.220, G.221, R.225 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.221, F:R.225 GOL.41: 7 residues within 4Å: Chain E: V.263 Chain G: C.6, A.7, T.8 Chain H: C.11, A.12 Ligands: SO4.26 1 PLIP interactions: 1 interactions with chain E Water bridges: E:V.263

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.15: 7 residues within 4Å: Chain A: Q.189, Y.215, R.332 Chain D: A.17 Ligands: XZ4.3, SO4.8, HEZ.16 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.332 MES.36: 7 residues within 4Å: Chain E: Q.189, Y.215, R.332 Chain H: A.17 Ligands: XZ4.24, SO4.29, HEZ.37 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.215 Salt bridges: E:R.332

2 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.16: 6 residues within 4Å: Chain A: Y.215, V.330, A.331, H.341, R.365 Ligands: MES.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.215, A:A.331 Hydrogen bonds: A:A.331, A:H.341, A:R.365, A:R.365 HEZ.37: 6 residues within 4Å: Chain E: Y.215, V.330, A.331, H.341, R.365 Ligands: MES.36 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:Y.215, E:A.331 Hydrogen bonds: E:A.331, E:H.341, E:R.365, E:R.365

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
A

B
B

E
A

F
B

Integrase

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