SMTL ID : 6vod.1

HIV-1 wild type protease with GRL-052-16A, a tricyclic cyclohexane fused tetrahydrofuranofuran (CHf-THF) derivative as the P2 ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

1 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

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 GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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

1 x T1R: (1R,3aS,5R,6S,7aR)-octahydro-1,6-epoxy-2-benzofuran-5-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate(Non-covalent)

T1R.4: 24 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, V.32, 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 23 PLIP interactions: 10 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:A.28, A:V.32, A:P.81, A:V.82, A:I.84, B:L.23, B:V.32, B:I.47, B:I.47, B:V.82 Hydrogen bonds: A:D.29, A:D.30, B:G.27, B:G.27, B:G.27, B:D.29, B:D.30 Water bridges: A:I.50, A:I.50, B:I.50, B:I.50 Salt bridges: A:D.25, B:D.25

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

FMT.6: 3 residues within 4Å: Chain B: S.37, L.38, Y.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.38, B:Y.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Structure-Based Design of Highly Potent HIV-1 Protease Inhibitors Containing New Tricyclic Ring P2-Ligands: Design, Synthesis, Biological, and X-ray Structural Studies. J.Med.Chem. (2020)

Release Date

2020-05-13

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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