SMTL ID : 8esx.1

HIV protease in complex with benzoxaborolone analog of darunavir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: Q.18, M.36, S.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.18, A:S.37

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: W.42, P.44, K.55 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Chain A: D.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 Water bridges: A:R.41

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: T.12, K.14, E.65, A.67, G.68 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.12 Hydrogen bonds: A:T.12, A:G.68

1 x X7B: [(3~{a}~{S},4~{R},6~{a}~{R})-2,3,3~{a},4,5,6~{a}-hexahydrofuro[2,3-b]furan-4-yl] ~{N}-[(2~{S},3~{R})-4-[[7,7-bis(oxidanyl)-9-oxidanylidene-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-3-yl]sulfonyl-(2-methylpropyl)amino]-3-oxidanyl-1-phenyl-butan-2-yl]carbamate(Non-covalent)

X7B.7: 27 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, L.76, P.81, V.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, V.82, I.84 22 PLIP interactions: 15 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:I.47, A:P.81, A:V.82, A:I.84, B:L.23, B:V.82 Hydrogen bonds: A:R.8, A:D.29, A:D.30, A:D.30, A:G.48, B:D.25, B:G.27, B:D.29, B:D.30 Water bridges: A:D.29, A:I.50, A:I.50 Salt bridges: A:D.25, B:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Graham, B.J. et al., Inhibition of HIV-1 Protease by a Boronic Acid with High Oxidative Stability. Acs Med.Chem.Lett. (2023)

Release Date

2023-02-08

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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