SMTL ID : 8cta.4 (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 17 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: A:A.120, A:T.125, B:Q.46, B:T.76, B:A.79, B:W.83, D:I.50, D:I.50 Hydrogen bonds: A:E.121, A:H.122, A:H.122, A:T.125, D:K.48 Salt bridges: A:H.122, D:K.48 pi-Stacking: D:W.17 pi-Cation interactions: D:K.48 L3D.3: 16 residues within 4Å: Chain A: Q.46, L.53, T.75, 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: 5 interactions with chain A, 5 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: A:T.75, A:T.76, A:A.79, A:A.80, A:W.83, C:I.50, C:I.50, B:T.125 Salt bridges: C:K.48, B:H.122 pi-Stacking: C:W.17 pi-Cation interactions: C:K.48 Hydrogen bonds: B:E.121, B:H.122, B:T.125, B:T.125

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

EDO.2: 2 residues within 4Å: Chain A: E.20, R.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.20, A:R.117 EDO.4: 5 residues within 4Å: Chain B: C.81, W.82, I.86, K.87, Q.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.88 EDO.5: 8 residues within 4Å: Chain A: L.53, K.54, G.57, R.58 Chain B: I.35, E.36, Q.128, V.131 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.53, A:G.57, A:R.58, B:F.132 EDO.6: 8 residues within 4Å: Chain A: A.79, W.82, W.83 Chain C: R.6, Y.8, I.50, R.51, D.52 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:A.79, A:W.83, C:R.6, C:Y.8, C:I.50, C:D.52 EDO.7: 9 residues within 4Å: Chain B: A.79, W.82, W.83 Chain D: N.4, R.6, Y.8, I.50, R.51, D.52 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.6, D:Y.8, D:R.51

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
M

B
N

C
O

D
P

Integrase

Integrase

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