SMTL ID : 9b2h.1

HIV-1 wild type protease with GRL-072-17A, a substituted tetrahydrofuran derivative based on Darunavir as P2 group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 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.7: 1 residues within 4Å: Chain B: D.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.60, B:D.60

4 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.8: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: I.47, G.48 Ligands: 01.6 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain A: G.52 Ligands: GOL.10 No protein-ligand interaction detected (PLIP) GOL.10: 6 residues within 4Å: Chain A: I.50, G.51, G.52 Chain B: I.54, P.79 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.51

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

FMT.5: 3 residues within 4Å: Chain A: G.48, F.53 Ligands: 01.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.48, A:G.48

1 x 01: 2,5:6,9-dianhydro-1,3,7,8-tetradeoxy-4-O-({(2S,3R)-3-hydroxy-4-[(4-methoxybenzene-1-sulfonyl)(2-methylpropyl)amino]-1-phenylbutan-2-yl}carbamoyl)-L-gluco-nonitol

01.6: 30 residues within 4Å: Chain A: 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 Chain B: R.8, L.23, 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 Ligands: FMT.5, CL.9 26 PLIP interactions: 12 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:V.32, B:I.50, B:P.81, B:P.81, B:V.82, B:I.84, A:L.23, A:A.28, A:V.32, A:V.82, A:I.84 Hydrogen bonds: B:D.29, B:D.30, A:G.27, A:G.27, A:G.27, A:D.29, A:D.30 Water bridges: B:I.50, A:I.50, A:I.50, A:I.50 Salt bridges: B:D.25, A:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Design of substituted tetrahydrofuran derivatives for HIV-1 protease inhibitors: synthesis, biological evaluation, and X-ray structural studies. Org.Biomol.Chem. (2024)

Release Date

2024-07-24

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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