SMTL ID : 6vce.1

HIV-1 wild type protease with GRL-026-18A, a crown-like tetrahydropyranotetrahydrofuran with a bridged methylene group as a P2 ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.18 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

6 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.3: 2 residues within 4Å: Chain A: K.7, R.8 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: I.54, K.55 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 CL.8: 4 residues within 4Å: Chain B: V.11, T.12, A.67 Ligands: GOL.9 Ligand excluded by PLIP

1 x G6R: N-[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]-2-[(3S,3aR,5S,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl]acetamide(Non-covalent)

G6R.5: 25 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, I.84 Chain B: R.8, D.25, G.27, A.28, D.29, D.30, V.32, K.45, G.48, G.49, I.50, P.81, V.82, I.84 23 PLIP interactions: 10 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:A.28, B:V.32, B:I.84, A:L.23, A:A.28, A:I.47, A:I.47, A:I.50, A:I.84 Hydrogen bonds: B:D.29, B:D.30, B:D.30, A:D.25, A:G.27, A:D.29, A:D.30, A:D.30 Water bridges: B:R.8, B:I.50, A:I.50 Salt bridges: B:D.25, A:D.25 Halogen bonds: B:R.8

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain B: T.12, E.65, A.67, G.68 Ligands: CL.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.68 Water bridges: B:T.12 GOL.10: 2 residues within 4Å: Chain B: P.39, G.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.40 Water bridges: B:L.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Design, Synthesis, and X-ray Studies of Potent HIV-1 Protease Inhibitors with P2-Carboxamide Functionalities. Acs Med.Chem.Lett. (2020)

Release Date

2020-07-01

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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