SMTL ID : 8zha.1

HIV-1 integrase core domain in complex with compound 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 6 residues within 4Å: Chain A: H.125, K.127 Chain B: Q.49, E.50, Y.53 Ligands: 01.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.127 Water bridges: A:V.42 PG4.5: 6 residues within 4Å: Chain A: Q.49, E.50, Y.53 Chain B: H.125, K.127 Ligands: 01.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.127 Water bridges: B:V.42

2 x 01: (2~{S})-2-[7-(cycloheptylcarbamoyl)-4',5-dimethyl-spiro[1,2-dihydroindene-3,1'-cyclohexane]-4-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid

01.2: 13 residues within 4Å: Chain A: Q.49, L.56, T.78, T.79, A.82, A.83, W.86 Chain B: Q.122, A.123, E.124, H.125, T.128 Ligands: PG4.5 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.56, A:T.79, A:A.82, A:W.86, B:T.128 Hydrogen bonds: B:E.124, B:H.125, B:T.128, B:T.128 Salt bridges: B:H.125 01.6: 13 residues within 4Å: Chain A: Q.122, A.123, E.124, H.125, T.128 Chain B: Q.49, L.56, T.78, T.79, A.82, A.83, W.86 Ligands: PG4.1 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.128, B:L.56, B:T.79, B:A.82, B:W.86 Hydrogen bonds: A:E.124, A:H.125, A:T.128 Salt bridges: A:H.125

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: K.25, R.120, E.124, H.125, L.126 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.120, A:L.126 Water bridges: A:K.25, A:K.25, A:K.127 Salt bridges: A:K.25, A:H.125 SO4.4: 3 residues within 4Å: Chain A: T.20, H.21, K.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.20, A:H.21 Salt bridges: A:H.21, A:K.113 SO4.7: 5 residues within 4Å: Chain B: K.25, R.120, E.124, H.125, L.126 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.120, B:L.126 Water bridges: B:K.25, B:K.25, B:K.127 Salt bridges: B:K.25, B:H.125 SO4.8: 3 residues within 4Å: Chain B: T.20, H.21, K.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.21 Water bridges: B:H.21 Salt bridges: B:H.21, B:K.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adachi, K. et al., Design and synthesis of novel and potent allosteric HIV-1 integrase inhibitors with a spirocyclic moiety. Bioorg.Med.Chem.Lett. (2024)

Release Date

2024-07-10

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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