SMTL ID : 8t5b.1

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor EKC-110

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

hetero-2-2-mer

Ligands

2 x QD6: (2S)-tert-butoxy{4-(4-chlorophenyl)-2,6-dimethyl-1-[(1-methyl-1H-pyrazol-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-5-yl}acetic acid(Non-covalent)

QD6.1: 21 residues within 4Å: Chain A: Q.112, A.113, E.114, H.115, K.117, T.118, M.122 Chain B: Q.39, A.42, Y.43, L.46, S.67, T.68, T.69, A.72, A.73, W.76 Chain D: Y.6, W.15, K.46, I.48 14 PLIP interactions: 5 interactions with chain A, 6 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: A:T.118, D:Y.6, D:W.15, D:W.15, B:Q.39, B:A.72, B:A.73 Hydrogen bonds: A:E.114, A:H.115, A:T.118 Salt bridges: A:H.115, D:K.46 pi-Stacking: D:W.15 pi-Cation interactions: D:K.46 QD6.3: 21 residues within 4Å: Chain A: Q.39, A.42, Y.43, L.46, S.67, T.68, T.69, A.72, A.73, W.76 Chain B: Q.112, A.113, E.114, H.115, K.117, T.118, M.122 Chain C: Y.6, W.15, K.46, I.48 17 PLIP interactions: 6 interactions with chain C, 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: C:Y.6, C:W.15, A:Q.39, A:T.69, A:A.72, A:A.73, B:T.118 Hydrogen bonds: C:K.46, B:E.114, B:H.115, B:T.118, B:T.118 Salt bridges: C:K.46, B:H.115 pi-Stacking: C:W.15 pi-Cation interactions: C:K.46 Water bridges: A:Q.39

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.8, C.9, D.60 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.8, A:D.60 MG.4: 4 residues within 4Å: Chain B: D.8, C.9, D.60, F.65 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.8, B:D.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dinh, T. et al., The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir. Biorxiv (2024)

Release Date

2024-06-19

Peptides

Integrase: AB
Integrase: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Integrase

Integrase