SMTL ID : 6u7p.1

HIV-1 wild type protease with GRL-03119A, with phenyl-boronic-acid as P2'-ligand and with a hexahydro-4H-furo-pyran as the P2-ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

homo-dimer

Ligands

1 x B4R: {4-[{(2R,3S)-3-[({[(3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-yl]oxy}carbonyl)amino]-2-hydroxy-4-phenylbutyl}(2-methylpropyl)sulfamoyl]phenyl}boronic acid(Non-covalent)

B4R.1: 24 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, 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 25 PLIP interactions: 10 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:L.23, B:V.82, A:A.28, A:V.32, A:I.50, A:P.81, A:V.82, A:I.84 Hydrogen bonds: B:D.25, B:G.27, B:G.27, B:D.29, B:D.30, A:D.29, A:D.30, A:D.30, A:D.30 Water bridges: B:I.50, B:I.50, A:G.48, A:G.48, A:I.50, A:I.50 Salt bridges: B:D.25, A:D.25

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

NA.2: 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

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

CL.3: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: K.7, R.8 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: V.11, T.12, A.67 Ligands: GOL.9 Ligand excluded by PLIP

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.8: 5 residues within 4Å: Chain B: M.36, S.37, L.38, R.57, Y.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.38, B:L.38, B:R.57

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain B: T.12, E.65, A.67, G.68 Ligands: CL.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.68 Water bridges: B:A.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Potent HIV-1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein-Ligand X-ray Structural Studies. Chemmedchem (2019)

Release Date

2019-10-09

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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