SMTL ID : 8cbs.1

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT871

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: V.16, W.17 Chain B: Q.116, T.145, T.146 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.116, A:W.17 Water bridges: B:T.145, B:T.146 EDO.2: 4 residues within 4Å: Chain A: N.4, F.5, R.6 Chain B: W.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.5, A:F.5, A:R.6 EDO.4: 6 residues within 4Å: Chain B: E.113, T.114, G.115, S.140, N.141 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.113, B:G.115 Water bridges: B:Q.116 EDO.5: 3 residues within 4Å: Chain B: K.206, S.216, E.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.216, B:S.216 EDO.6: 6 residues within 4Å: Chain B: V.186, Q.189, M.199 Chain C: R.51, Y.53 Chain D: W.153 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: B:Q.189, D:W.153, C:R.51, C:R.51 EDO.7: 4 residues within 4Å: Chain B: S.140, T.143, S.144 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.143, B:T.143 EDO.10: 4 residues within 4Å: Chain B: I.203, K.206, K.207 Chain C: Y.53 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:I.203, C:Y.53 EDO.11: 2 residues within 4Å: Chain C: L.23, L.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.24 EDO.13: 6 residues within 4Å: Chain A: Y.53 Chain B: W.153 Chain D: V.186, Q.189, M.199, I.203 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:Q.189, B:W.153 Water bridges: A:R.51 EDO.14: 2 residues within 4Å: Chain D: E.90, K.92 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.90, D:E.90 EDO.15: 5 residues within 4Å: Chain D: E.113, T.114, G.115, S.140, N.141 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.115 Water bridges: D:Q.116, D:S.140, D:S.144, D:T.146 EDO.16: 2 residues within 4Å: Chain D: G.184, R.187 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.184 Water bridges: D:R.187 EDO.17: 4 residues within 4Å: Chain D: C.86, T.87, H.88, N.176 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.176 Water bridges: D:H.88, D:K.180 EDO.19: 2 residues within 4Å: Chain D: H.192, K.194 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.192, D:K.194 Water bridges: D:L.193

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: G.27, E.28, G.29, A.30 Ligand excluded by PLIP

2 x U5L: (2~{S})-2-[3-cyclopropyl-6-methyl-2-(5-methyl-3,4-dihydro-2~{H}-chromen-6-yl)phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid(Non-covalent)

U5L.8: 17 residues within 4Å: Chain B: Q.189, A.190, E.191, H.192, T.195, M.199 Chain C: Y.8, W.17, K.48, I.50 Chain D: Q.116, L.123, T.145, T.146, A.149, A.150, W.153 20 PLIP interactions: 5 interactions with chain D, 5 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: D:Q.116, D:T.146, D:A.149, D:A.150, D:W.153, B:T.195, C:Y.8, C:W.17, C:W.17, C:W.17, C:K.48, C:K.48, C:I.50, C:I.50 Hydrogen bonds: B:E.191, B:H.192, B:T.195 Salt bridges: B:H.192, C:K.48 pi-Cation interactions: C:K.48 U5L.12: 15 residues within 4Å: Chain A: Y.8, W.17, K.48 Chain B: Q.116, L.123, T.146, A.149, A.150, W.153 Chain D: Q.189, A.190, E.191, H.192, T.195, M.199 16 PLIP interactions: 6 interactions with chain D, 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: D:T.195, B:Q.116, B:T.146, B:A.149, B:A.150, B:W.153, A:Y.8, A:W.17 Hydrogen bonds: D:E.191, D:H.192, D:T.195, D:T.195 Salt bridges: D:H.192, A:K.48 pi-Stacking: A:W.17 pi-Cation interactions: A:K.48

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain B: D.85, D.137 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.85, B:D.137, H2O.2, H2O.2, H2O.3 MG.18: 2 residues within 4Å: Chain D: D.85, D.137 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.85, D:D.137, H2O.7, H2O.7, H2O.7, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonnard, D. et al., Biological and Structural Analyses of New Potent Allosteric Inhibitors of HIV-1 Integrase. Antimicrob.Agents Chemother. (2023)

Release Date

2023-06-07

Peptides

Integrase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Integrase

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