SMTL ID : 6e9a.1

HIV-1 WILD TYPE PROTEASE WITH GRL-034-17A, (3aS, 5R, 6aR)-2-OXOHEXAHYD CYCLOPENTA[D]-5-OXAZOLYL URETHANE WITH A BICYCLIC OXAZOLIDINONE SCAFF AS THE P2 LIGAND

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 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 NA.4: 1 residues within 4Å: Chain B: D.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.60, B:D.60

2 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: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP

1 x J0S: (3aS,5R,6aR)-2-oxohexahydro-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)

J0S.3: 26 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, I.47, G.48, G.49, I.50, V.82, I.84 19 PLIP interactions: 11 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.23, B:V.32, B:V.82, A:A.28, A:V.32, A:I.50, A:P.81, A:V.82 Hydrogen bonds: B:D.25, B:G.27, B:D.29, B:G.48, A:D.29, A:D.30 Water bridges: B:G.48, B:I.50, B:I.50 Salt bridges: B:D.25, A:D.25

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

FMT.6: 1 residues within 4Å: Chain B: Q.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.61 Water bridges: B:Q.61

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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