SMTL ID : 6cdj.1

HIV-1 wild type protease with GRL-03314A, 6-5-5-ring fused umbrella-like tetrahydropyranofuran as the P2-ligand, a cyclopropylaminobenzothiazole as the P2'-ligand and 3,5-difluorophenylmethyl as the P1-ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

homo-dimer

Ligands

1 x GR8: (2aS,4R,4aS,7aS,7bS)-octahydro-2H-1,7-dioxacyclopenta[cd]inden-4-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate(Non-covalent)

GR8.1: 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, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, P.81, V.82, I.84 Ligands: GOL.4 20 PLIP interactions: 11 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:V.32, A:I.47, A:I.84, B:L.23, B:A.28, B:V.32, B:I.84 Hydrogen bonds: A:D.25, A:G.27, A:G.27, A:D.29, A:D.30, B:D.29, B:D.30, B:D.30, B:I.50 Water bridges: A:I.50, A:I.50 Salt bridges: A:D.25, B:D.25

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

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

3 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.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

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: G.48, F.53 Chain B: R.8 Ligands: GR8.1 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:G.48, A:G.48 Hydrogen bonds: B:R.8, B:R.8

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

ACT.7: 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 ACT.8: 5 residues within 4Å: Chain B: P.39, G.40, R.41, Y.59, D.60 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.60 Hydrogen bonds: B:D.60 Water bridges: B:R.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Design and Synthesis of Highly Potent HIV-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems as Novel P2 Ligands: Structure-Activity Studies, Biological and X-ray Structural Analysis. J. Med. Chem. (2018)

Release Date

2018-05-30

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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