SMTL ID : 5mmb.1

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ434 (compound 6p)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-tetramer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.3, OUY.17 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.188, H2O.1, H2O.4 MG.3: 5 residues within 4Å: Chain A: D.131, E.224, N.227 Ligands: MG.2, OUY.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.4 MG.20: 2 residues within 4Å: Chain B: D.131, D.188 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.131, B:D.188 MG.26: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.27, OUY.41 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.5, H2O.8 MG.27: 5 residues within 4Å: Chain E: D.131, E.224, N.227 Ligands: MG.26, OUY.41 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.131, E:E.224, E:E.224, H2O.8 MG.44: 2 residues within 4Å: Chain F: D.131, D.188 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.131, F:D.188

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

SO4.4: 4 residues within 4Å: Chain A: P.138, S.139, Q.140, K.244 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: G.190, A.191 Chain D: A.17 Ligands: OUY.17 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: S.335, L.336, R.339 Chain E: K.231 Chain H: C.16 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: H.341, K.342, H.360 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: T.161, K.162, A.168 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: Q.63, L.82, Y.83 Chain E: F.281 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: N.174, T.177, R.205 Chain B: P.250, L.254 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain A: R.117, Y.306, P.308 Chain C: C.6 Ligands: GOL.24 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain B: K.222, R.225, S.261, P.262, V.263 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain E: P.138, S.139, Q.140, K.244 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain E: G.190, A.191 Chain H: A.17 Ligands: OUY.41 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain A: K.231 Chain D: C.16 Chain E: S.335, L.336, R.339 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain E: H.341, K.342, H.360 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain E: T.161, K.162, A.168 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain A: F.281 Chain E: Q.63, L.82, Y.83 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain E: N.174, T.177, R.205 Chain F: P.250, L.254 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain E: R.117, Y.306, P.308 Chain G: C.6 Ligands: GOL.48 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain F: K.222, R.225, S.261, P.262, V.263 Ligand excluded by PLIP

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 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.13: 3 residues within 4Å: Chain A: P.118, D.119 Chain C: T.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.119 GOL.14: 2 residues within 4Å: Chain A: H.22, Y.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.23 GOL.15: 6 residues within 4Å: Chain A: R.337, R.339 Chain E: S.228, T.235 Chain H: A.15, C.16 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.228, E:T.235, A:R.339 Water bridges: A:R.339 GOL.16: 7 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, I.275, D.276 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.274, B:D.276 GOL.22: 2 residues within 4Å: Chain B: S.220, G.221 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.221, B:R.225 GOL.24: 7 residues within 4Å: Chain A: V.263 Chain C: C.6, A.7, T.8 Chain D: C.11, A.12 Ligands: SO4.11 No protein-ligand interaction detected (PLIP) GOL.36: 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.37: 3 residues within 4Å: Chain E: P.118, D.119 Chain G: T.3 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.119 GOL.38: 2 residues within 4Å: Chain E: H.22, Y.23 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.22, E:Y.23 GOL.39: 6 residues within 4Å: Chain A: S.228, T.235 Chain D: A.15, C.16 Chain E: R.337, R.339 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:S.228, A:T.235, A:T.235, E:R.339 Water bridges: E:R.339 GOL.40: 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:G.274, F:D.276, F:D.276 GOL.46: 2 residues within 4Å: Chain F: S.220, G.221 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.221, F:R.225 GOL.48: 7 residues within 4Å: Chain E: V.263 Chain G: C.6, A.7, T.8 Chain H: C.11, A.12 Ligands: SO4.35 No protein-ligand interaction detected (PLIP)

2 x OUY: methyl 3-[5-azanyl-6-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-8-oxidanyl-7-oxidanylidene-1,8-naphthyridin-3-yl]propanoate(Non-covalent)

OUY.17: 14 residues within 4Å: Chain A: D.131, D.188, Q.189, Y.215, P.217, Q.218, E.224, R.332 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.2, MG.3, SO4.5 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 Salt bridges: A:R.332 Halogen bonds: A:E.224 OUY.41: 14 residues within 4Å: Chain E: D.131, D.188, Q.189, Y.215, P.217, Q.218, E.224, R.332 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.26, MG.27, SO4.29 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 Salt bridges: E:R.332 Halogen bonds: E:E.224

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

HEZ.18: 6 residues within 4Å: Chain A: W.318, P.374, T.375, H.377, Q.378 Chain G: G.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.374 Hydrogen bonds: A:T.375, A:H.377, A:Q.378 HEZ.19: 7 residues within 4Å: Chain A: Y.260, K.265, Y.266, Q.270, G.274, N.283, I.301 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.266, A:Q.270 HEZ.23: 7 residues within 4Å: Chain A: V.175, S.178 Chain B: L.158, Y.159, Y.246, P.250, Q.253 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.158, B:Y.246, B:Q.253 Hydrophobic interactions: A:V.175 HEZ.42: 6 residues within 4Å: Chain C: G.10 Chain E: W.318, P.374, T.375, H.377, Q.378 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:P.374 Hydrogen bonds: E:T.375, E:H.377, E:Q.378 HEZ.43: 7 residues within 4Å: Chain E: Y.260, K.265, Y.266, Q.270, G.274, N.283, I.301 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.266, E:Q.270 HEZ.47: 7 residues within 4Å: Chain E: V.175, S.178 Chain F: L.158, Y.159, Y.246, P.250, Q.253 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:L.158, F:Y.246, F:Q.253 Hydrophobic interactions: E:V.175

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

PFV INTEGRASE: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

PFV INTEGRASE

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