SMTL ID : 8bv2.1

Biological and structural analysis of new potent Integrase-LEDGF allosteric HIV-1 inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x RWR: (2S)-2-[3-cyclopropyl-2-(3,4-dihydro-2H-chromen-6-yl)-6-methyl-phenyl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid(Non-covalent)

RWR.1: 13 residues within 4Å: Chain A: Q.65, L.72, T.94, T.95, A.98, A.99, W.102 Chain B: Q.138, A.139, E.140, H.141, T.144, M.148 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.144, A:Q.65, A:T.94, A:T.95, A:A.98, A:A.98, A:W.102 Hydrogen bonds: B:E.140, B:H.141, B:T.144 Salt bridges: B:H.141 RWR.4: 13 residues within 4Å: Chain A: Q.138, A.139, E.140, H.141, T.144, M.148 Chain B: Q.65, L.72, T.94, T.95, A.98, A.99, W.102 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.144, B:Q.65, B:T.94, B:T.95, B:A.98, B:A.98, B:W.102 Hydrogen bonds: A:E.140, A:H.141, A:T.144, A:T.144 Salt bridges: A:H.141

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.34, C.35, N.90 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: D.34, C.35, N.90 No protein-ligand interaction detected (PLIP)

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

SO4.3: 5 residues within 4Å: Chain A: K.41, R.136, E.140, H.141, L.142 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.136, A:E.140, A:L.142 Water bridges: A:K.41, A:K.143 Salt bridges: A:K.41, A:H.141 SO4.6: 5 residues within 4Å: Chain B: K.41, R.136, E.140, H.141, L.142 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.136, B:E.140, B:L.142 Water bridges: B:K.41, B:K.143 Salt bridges: B:K.41, B:H.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonnard, D. et al., Biological and Structural Analyses of New Potent Allosteric Inhibitors of HIV-1 Integrase. Antimicrob.Agents Chemother. (2023)

Release Date

2023-06-07

Peptides

Integrase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Integrase

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