SMTL ID : 4ikf.1

PFV intasome with inhibitor MB-76

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 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.13: 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

4 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: 5 residues within 4Å: Chain B: K.222, R.225, S.261, P.262, V.263 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.263 Salt bridges: B:K.222, B:R.225 SO4.14: 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 SO4.22: 5 residues within 4Å: Chain F: K.222, R.225, S.261, P.262, V.263 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:V.263 Salt bridges: F:K.222, F:R.225

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

NH4.3: 3 residues within 4Å: Chain A: P.118, D.119 Chain C: T.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.119, A:D.119 NH4.15: 3 residues within 4Å: Chain E: P.118, D.119 Chain G: T.3 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.119, E:D.119

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: D.131, Y.132, D.188 Chain D: A.17 Ligands: MG.5, M76.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.131, A:D.188, A:D.188 MG.5: 6 residues within 4Å: Chain A: D.131, E.224, N.227 Chain D: A.17 Ligands: MG.4, M76.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.131, A:E.224, A:E.224 MG.16: 6 residues within 4Å: Chain E: D.131, Y.132, D.188 Chain H: A.17 Ligands: MG.17, M76.24 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.131, E:D.188, E:D.188 MG.17: 6 residues within 4Å: Chain E: D.131, E.224, N.227 Chain H: A.17 Ligands: MG.16, M76.24 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.131, E:E.224, E:E.224

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: S.165, T.166, S.167, A.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.166, A:T.166, A:S.167, A:A.191 GOL.7: 5 residues within 4Å: Chain A: P.138, S.139, Q.140, T.243, K.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.140, A:T.243 GOL.8: 6 residues within 4Å: Chain A: Q.63, L.82, Y.83 Chain E: T.279, P.280, F.281 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:T.279, E:F.281, A:Q.63, A:Q.63, A:Y.83 GOL.9: 6 residues within 4Å: Chain A: L.295 Chain B: Y.266, Q.270, G.274, I.275, D.276 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.270, B:G.274, B:D.276, A:Q.299 GOL.18: 4 residues within 4Å: Chain E: S.165, T.166, S.167, A.191 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.166, E:S.167, E:A.191 GOL.19: 5 residues within 4Å: Chain E: P.138, S.139, Q.140, T.243, K.244 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.140, E:T.243 GOL.20: 6 residues within 4Å: Chain A: T.279, P.280, F.281 Chain E: Q.63, L.82, Y.83 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:T.279, A:F.281, E:Q.63, E:Q.63, E:Y.83, E:Y.83 GOL.21: 6 residues within 4Å: Chain E: L.295 Chain F: Y.266, Q.270, G.274, I.275, D.276 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Q.270, F:G.274, F:D.276, E:Q.299

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

HEZ.11: 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: 4 interactions with chain B Hydrophobic interactions: B:Y.159 Hydrogen bonds: B:Y.159, B:Y.246, B:Q.253 HEZ.23: 7 residues within 4Å: Chain E: V.175, S.178 Chain F: L.158, Y.159, Y.246, P.250, Q.253 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:Y.159 Hydrogen bonds: F:Y.246, F:Q.253

2 x M76: N-(4-fluorobenzyl)-2,3-dihydroxy-1-oxo-1,2-dihydroisoquinoline-4-carboxamide(Non-covalent)

M76.12: 11 residues within 4Å: Chain A: D.131, Y.132, D.188, P.217, Q.218, E.224 Chain C: G.4 Chain D: C.16, A.17 Ligands: MG.4, MG.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.217, A:E.224 M76.24: 11 residues within 4Å: Chain E: D.131, Y.132, D.188, P.217, Q.218, E.224 Chain G: G.4 Chain H: C.16, A.17 Ligands: MG.16, MG.17 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:P.217, E:E.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Desimmie, B.A. et al., 2-Hydroxyisoquinoline-1,3(2H,4H)-diones (HIDs), novel inhibitors of HIV integrase with a high barrier to resistance. Acs Chem.Biol. (2013)

Release Date

2013-04-03

Peptides

Integrase: ABEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
A

F
B

Integrase

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