SMTL ID : 4be1.1

PFV intasome with inhibitor XZ-116

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 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.14: 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 SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: H.341, K.342, H.360 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.342 Salt bridges: A:H.341, A:K.342, A:H.360 SO4.10: 6 residues within 4Å: Chain A: D.188, Q.189, G.190, P.214, Y.215 Ligands: CI4.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.189, A:Y.215 SO4.11: 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 SO4.15: 3 residues within 4Å: Chain E: H.341, K.342, H.360 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.342 Salt bridges: E:H.341, E:K.342, E:H.360 SO4.23: 6 residues within 4Å: Chain E: D.188, Q.189, G.190, P.214, Y.215 Ligands: CI4.22 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.189, E:Y.215 SO4.24: 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

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 2 residues within 4Å: Chain A: P.118, D.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.119, A:D.119 NH4.16: 2 residues within 4Å: Chain E: P.118, D.119 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.119, E:D.119

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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.5: 3 residues within 4Å: Chain A: S.139, Q.140, K.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.140 GOL.6: 5 residues within 4Å: Chain A: Q.63, L.82, Y.83 Chain E: P.280, F.281 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:F.281 GOL.12: 7 residues within 4Å: Chain A: L.295, Q.299 Chain B: Y.266, Q.270, G.274, I.275, D.276 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.270, B:D.276, A:Q.299 GOL.17: 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.18: 3 residues within 4Å: Chain E: S.139, Q.140, K.244 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.140 GOL.19: 5 residues within 4Å: Chain A: P.280, F.281 Chain E: Q.63, L.82, Y.83 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:F.281, E:Y.83 GOL.25: 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: 2 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Q.270, F:D.276, E:Q.299

6 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: D.131, D.188 Ligands: MG.8, CI4.9 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.8: 5 residues within 4Å: Chain A: D.131, E.224, N.227 Ligands: MG.7, CI4.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.131, A:E.224, A:E.224, H2O.3 MG.13: 2 residues within 4Å: Chain B: D.131, D.188 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.131, B:D.188, H2O.7, H2O.7 MG.20: 4 residues within 4Å: Chain E: D.131, D.188 Ligands: MG.21, CI4.22 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.188, H2O.12, H2O.12 MG.21: 5 residues within 4Å: Chain E: D.131, E.224, N.227 Ligands: MG.20, CI4.22 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.26: 2 residues within 4Å: Chain F: D.131, D.188 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.131, F:D.188, H2O.16, H2O.16

2 x CI4: 2-(3-chloro-2-fluorobenzyl)-6,7-dihydroxy-2,3-dihydro-1H-isoindol-1-one(Non-covalent)

CI4.9: 11 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.7, MG.8, SO4.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.131, A:N.227 CI4.22: 11 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.20, MG.21, SO4.23 2 PLIP interactions: 2 interactions with chain E Water bridges: E:D.188, E:N.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Metifiot, M. et al., Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase. Acs Chem.Biol. (2013)

Release Date

2012-10-31

Peptides

INTEGRASE: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

INTEGRASE

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