SMTL ID : 8cta.2 (3 other biounits)

Minimal 2:2 Ternary Complex between BI-224436 bound HIV-1 Integrase Catalytic Core Domain Dimer and Carboxy Terminal Domains

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

hetero-2-2-mer

Ligands

2 x L3D: (2S)-tert-butoxy[4-(2,3-dihydropyrano[4,3,2-de]quinolin-7-yl)-2-methylquinolin-3-yl]acetic acid(Non-covalent)

L3D.1: 15 residues within 4Å: Chain A: Q.119, A.120, E.121, H.122, T.125, M.129 Chain B: Q.46, L.53, T.76, A.79, A.80, W.83 Chain D: W.17, K.48, I.50 20 PLIP interactions: 6 interactions with chain D, 6 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: D:I.50, B:Q.46, B:T.76, B:A.79, B:A.80, B:W.83, A:A.120, A:E.121, A:T.125 Hydrogen bonds: D:K.48, B:Q.46, A:E.121, A:H.122, A:H.122, A:T.125 Salt bridges: D:K.48, A:H.122 pi-Stacking: D:W.17, D:W.17 pi-Cation interactions: D:K.48 L3D.6: 15 residues within 4Å: Chain A: Q.46, L.53, T.76, A.79, A.80, W.83 Chain B: Q.119, A.120, E.121, H.122, T.125, M.129 Chain C: W.17, K.48, I.50 16 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: A:T.76, A:A.79, A:W.83, C:I.50, B:A.120, B:T.125 Hydrogen bonds: C:K.48, B:E.121, B:H.122, B:H.122, B:T.125, B:T.125 Salt bridges: C:K.48, B:H.122 pi-Stacking: C:W.17 pi-Cation interactions: C:K.48

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

EDO.2: 6 residues within 4Å: Chain A: R.138, G.141, I.142, G.143, G.144, Y.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.141 EDO.3: 6 residues within 4Å: Chain A: K.78, C.81, W.82, I.86, K.87, Q.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.86, A:Q.88 EDO.4: 8 residues within 4Å: Chain A: G.148, E.149, V.152 Chain B: R.58, W.59, P.60, I.155 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.58 EDO.5: 7 residues within 4Å: Chain A: Q.128, V.131, F.132 Chain B: L.53, K.54, G.57, R.58 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.53, A:F.132 EDO.7: 4 residues within 4Å: Chain B: C.81, W.82, I.86, Q.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.88 EDO.8: 9 residues within 4Å: Chain A: N.135, K.136, G.148 Chain B: A.56, G.57, R.58, W.59, P.60 Ligands: EDO.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.136, A:K.136, B:W.59 Water bridges: A:S.146 EDO.9: 1 residues within 4Å: Chain B: H.65 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.65 EDO.10: 6 residues within 4Å: Chain B: E.36, E.38, F.51, K.54, L.55, R.58 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.36, B:E.38, B:K.54, B:R.58 EDO.11: 8 residues within 4Å: Chain A: A.79, W.82, W.83 Chain C: R.6, Y.8, I.50, R.51, D.52 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.8, C:Y.8, C:R.51, A:W.83 EDO.12: 8 residues within 4Å: Chain B: A.79, W.82, W.83 Chain D: R.6, Y.8, I.50, R.51, D.52 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.52, B:W.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eilers, G. et al., Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 angstrom resolution: Routes to inhibitor optimization. Plos Pathog. (2023)

Release Date

2023-02-22

Peptides

Integrase: AB
Integrase: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Integrase

Integrase

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