SMTL ID : 8f0f.1

HIV-1 wild type protease with GRL-110-19A, a chloroacetamide derivative based on Darunavir as P2' group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.29 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

3 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 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.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 X7H: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[4-(2-chloroacetamido)benzene-1-sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate(Non-covalent)

X7H.4: 27 residues within 4Å: Chain A: 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 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, V.82, I.84 28 PLIP interactions: 18 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:D.29, A:D.30, A:V.32, A:P.81, A:V.82, A:I.84, B:L.23, B:V.82 Hydrogen bonds: A:D.29, A:D.30, A:D.30, B:D.25, B:G.27, B:G.27, B:D.29, B:D.30 Water bridges: A:G.48, A:G.48, A:G.48, A:G.48, A:I.50, A:I.50, B:I.50, B:I.50 Salt bridges: A:D.25, B:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Evaluation of Darunavir-derived HIV-1 protease inhibitors incorporating P2' amide-derivatives: Synthesis, biological evaluation and structural studies. Bioorg.Med.Chem.Lett. (2023)

Release Date

2023-02-15

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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