SMTL ID : 8cta.3 (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: 14 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: K.48, I.50 17 PLIP interactions: 7 interactions with chain C, 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:K.48, C:I.50, C:I.50, B:A.120, B:T.125, A:A.79, A:W.83 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

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

EDO.2: 5 residues within 4Å: Chain A: K.78, C.81, W.82, I.86, Q.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.88 EDO.4: 5 residues within 4Å: Chain B: C.81, W.82, I.86, K.87, Q.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.88, B:Q.88 Water bridges: B:I.86 EDO.5: 1 residues within 4Å: Chain C: Y.53 No protein-ligand interaction detected (PLIP) 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 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.6, C:Y.8, C:Y.8, C:R.51, A:W.83 EDO.7: 8 residues within 4Å: Chain B: A.79, W.82, W.83 Chain D: 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 EDO.8: 2 residues within 4Å: Chain D: L.23, L.24 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.23 EDO.9: 1 residues within 4Å: Chain D: Y.53 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.53

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
I

B
J

C
K

D
L

Integrase

Integrase

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