SMTL ID : 8cbv.1

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor MUT916

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 5 residues within 4Å: Chain B: L.89, K.180, I.183, G.184, R.187 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.184 EDO.3: 6 residues within 4Å: Chain B: E.113, T.114, G.115, S.140, N.141 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.115, B:S.140 Water bridges: B:Q.116 EDO.4: 4 residues within 4Å: Chain B: S.140, T.143, S.144 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.143, B:T.143 EDO.5: 6 residues within 4Å: Chain A: R.51, Y.53 Chain B: V.186, Q.189, I.203 Chain D: W.153 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Water bridges: A:R.51, A:R.51 Hydrogen bonds: B:Q.189, D:W.153 EDO.8: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.113 EDO.9: 4 residues within 4Å: Chain C: F.5, L.23, K.26, I.49 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.26 EDO.12: 5 residues within 4Å: Chain D: G.91, K.92, V.93, I.110, P.111 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.93, D:V.93 Water bridges: D:K.92 EDO.13: 5 residues within 4Å: Chain B: R.128, P.130 Chain D: K.206, G.218, E.219 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.206, D:K.206, D:G.218 Water bridges: D:S.216 EDO.14: 4 residues within 4Å: Chain D: T.114, G.115, S.140, S.144 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.115, D:S.144 Water bridges: D:Q.116, D:Q.116, D:T.145, D:T.146 EDO.15: 6 residues within 4Å: Chain B: W.153 Chain C: Y.53 Chain D: V.186, Q.189, M.199, I.203 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.189, B:W.153

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

PEG.2: 7 residues within 4Å: Chain B: K.148, C.151, W.152, G.155, I.156 Chain C: D.52, K.55 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:W.152, B:G.155, C:K.55

2 x U5S: (2~{S})-2-[3-cyclopropyl-2-(8-fluoranyl-5-methyl-3,4-dihydro-2~{H}-chromen-6-yl)-6-methyl-phenyl]-2-cyclopropyloxy-ethanoic acid(Non-covalent)

U5S.6: 18 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, A.119, Y.120, L.123, T.146, A.149, A.150, W.153 17 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: A:Y.8, A:W.17, A:K.48, A:K.48, A:I.50, B:T.195, D:Q.116, D:Y.120, D:T.146, D:A.149, D:W.153 Salt bridges: A:K.48, B:H.192 pi-Cation interactions: A:K.48 Hydrogen bonds: B:E.191, B:H.192, B:T.195 U5S.11: 17 residues within 4Å: Chain B: Q.116, A.119, Y.120, L.123, T.145, T.146, A.149, A.150, W.153 Chain C: Y.8, W.17 Chain D: Q.189, A.190, E.191, H.192, T.195, M.199 13 PLIP interactions: 5 interactions with chain D, 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: D:E.191, D:H.192, D:T.195, D:T.195 Salt bridges: D:H.192 Hydrophobic interactions: B:Q.116, B:Y.120, B:T.146, B:A.149, B:W.153, C:Y.8, C:W.17 pi-Stacking: C:W.17

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 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.3, H2O.3 MG.16: 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.6, H2O.6, H2O.6, H2O.7

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

CL.10: 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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