SMTL ID : 8cbt.1

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT872

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

2 x W2Q: (2~{S})-2-[3-cyclopropyl-2-(3,4-dihydro-2~{H}-chromen-6-yl)-6-methyl-phenyl]-2-cyclopropyloxy-ethanoic acid(Non-covalent)

W2Q.1: 17 residues within 4Å: Chain A: Y.8, W.17, K.48, I.50 Chain B: Q.189, A.190, E.191, H.192, T.195, M.199 Chain D: Q.116, Y.120, T.146, A.149, A.150, W.153 Ligands: PEG.11 16 PLIP interactions: 7 interactions with chain A, 5 interactions with chain D, 4 interactions with chain B Hydrophobic interactions: A:Y.8, A:W.17, A:W.17, A:I.50, A:I.50, D:Q.116, D:Y.120, D:T.146, D:A.149, D:A.150, B:T.195 Salt bridges: A:K.48, B:H.192 pi-Cation interactions: A:K.48 Hydrogen bonds: B:E.191, B:H.192 W2Q.8: 19 residues within 4Å: Chain B: Q.116, Y.120, L.123, T.145, T.146, A.149, A.150, W.153 Chain C: Y.8, W.17, K.48, I.50 Chain D: Q.189, A.190, E.191, H.192, T.195, M.199 Ligands: PEG.5 17 PLIP interactions: 5 interactions with chain D, 7 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: D:T.195, C:Y.8, C:W.17, C:K.48, C:I.50, B:Y.120, B:L.123, B:T.146, B:A.149, B:A.150 Hydrogen bonds: D:E.191, D:H.192, D:T.195 Salt bridges: D:H.192, C:K.48 pi-Stacking: C:W.17 pi-Cation interactions: C:K.48

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

EDO.2: 5 residues within 4Å: Chain B: E.113, T.114, G.115, S.140, N.141 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.113, B:G.115 EDO.3: 4 residues within 4Å: Chain B: K.206, R.208, S.216, E.219 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.216, B:S.216 Water bridges: B:K.206 EDO.6: 2 residues within 4Å: Chain C: N.4, F.5 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.4, C:N.4, C:F.5 EDO.9: 4 residues within 4Å: Chain D: T.114, G.115, S.140, S.144 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.115 Water bridges: D:Q.116 EDO.10: 9 residues within 4Å: Chain B: F.202, K.206 Chain D: A.126, W.129, P.130, V.131, A.154, G.155, I.156 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:W.129, D:V.131, D:G.155

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain B: D.85, D.137 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.85, B:D.137, H2O.1, H2O.2, H2O.2, H2O.3 MG.14: 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.4, H2O.4, H2O.5, H2O.6

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 8 residues within 4Å: Chain B: W.153 Chain C: A.47, K.48, I.49, I.50 Chain D: Q.189, M.199 Ligands: W2Q.8 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:A.47, C:I.49, B:W.153 Water bridges: D:Q.189 PEG.11: 5 residues within 4Å: Chain B: K.194 Chain D: Q.116, E.117, Y.120 Ligands: W2Q.1 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:K.194, D:Q.116, D:Q.116 PEG.12: 6 residues within 4Å: Chain D: L.89, E.90, K.180, I.183, G.184, R.187 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.180 PEG.13: 6 residues within 4Å: Chain D: G.91, K.92, V.93, V.109, I.110, P.111 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.93, D:V.93

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

CL.7: 4 residues within 4Å: Chain C: G.27, E.28, G.29, A.30 Ligand excluded by PLIP

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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