SMTL ID : 6e7j.1

HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one with a bicyclic oxazolidinone scaffold as the P2 ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

1 x HWY: (3aS,5R,6aR)-2-oxo-3-phenylhexahydro-2H-cyclopenta[d][1,3]oxazol-5-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate(Non-covalent)

HWY.1: 24 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, D.30, G.48, G.49, I.50, V.82 Chain B: R.8, 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 20 PLIP interactions: 11 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.28, B:V.32, B:I.47, B:P.81, B:P.81, B:V.82, B:I.84, A:L.23, A:V.82 Hydrogen bonds: B:D.29, B:D.30, B:I.50, A:D.25, A:G.27, A:G.27, A:D.29 Salt bridges: B:D.25, A:D.25 Water bridges: A:I.50, A:I.50

2 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:R.41, A:D.60 Water bridges: A:R.41 NA.5: 1 residues within 4Å: Chain B: D.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.60

4 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.6: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Design and Synthesis of Potent HIV-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold as the P2 Ligands: Structure-Activity Studies and Biological and X-ray Structural Studies. J. Med. Chem. (2018)

Release Date

2018-11-07

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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