SMTL ID : 4kb9.1

Crystal structure of wild-type HIV-1 protease with novel tricyclic P2-ligands GRL-0739A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-dimer

Ligands

1 x G79: (3aR,3bR,4S,7aR,8aS)-decahydrofuro[2,3-b][1]benzofuran-4-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate(Non-covalent)

G79.1: 26 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, 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 20 PLIP interactions: 9 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:I.47, A:V.82, A:I.84, B:L.23, B:A.28, B:V.32, B:I.50, B:P.81, B:V.82 Hydrogen bonds: A:D.25, A:G.27, A:G.27, A:D.29, B:D.29, B:D.30 Water bridges: A:I.50, B:I.50 Salt bridges: A:D.25, B:R.8, B:D.25

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: W.6 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: G.73, T.74, N.88 Ligands: ACT.7 Ligand excluded by PLIP

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

ACT.3: 1 residues within 4Å: Chain A: P.44 No protein-ligand interaction detected (PLIP) ACT.4: 1 residues within 4Å: Chain A: P.44 No protein-ligand interaction detected (PLIP) ACT.7: 5 residues within 4Å: Chain B: D.29, D.30, T.74, N.88 Ligands: CL.6 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.88, B:N.88, B:N.88

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

NA.5: 1 residues within 4Å: Chain B: D.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.60

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain B: Q.18, M.36, S.37 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.18, B:S.37, B:S.37 GOL.9: 3 residues within 4Å: Chain B: K.45, M.46, F.53 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.46 Water bridges: B:G.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Highly Potent HIV-1 Protease Inhibitors with Novel Tricyclic P2 Ligands: Design, Synthesis, and Protein-Ligand X-ray Studies. J.Med.Chem. (2013)

Release Date

2013-09-04

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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