SMTL ID : 3h5b.1

Crystal structure of wild type HIV-1 protease with novel P1'-ligand GRL-02031

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.60

2 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.4: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP

1 x 031: (3aS,5R,6aR)-hexahydro-2H-cyclopenta[b]furan-5-yl [(1S,2R)-1-benzyl-2-hydroxy-3-([(4-methoxyphenyl)sulfonyl]{[(2R)-5-oxopyrrolidin-2-yl]methyl}amino)propyl]carbamate(Non-covalent)

031.3: 24 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, 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, I.47, G.48, G.49, I.50, P.81, I.84 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:V.32, B:I.50, B:P.81, B:I.84, A:I.84 Hydrogen bonds: B:G.27, B:D.29, B:D.30, B:I.50, A:D.25, A:G.27, A:D.29 Salt bridges: B:D.25 Water bridges: A:I.50, A:I.50

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain B: W.42, K.55, V.56, R.57 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.55, B:R.57 Water bridges: B:V.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Design of HIV-1 protease inhibitors with pyrrolidinones and oxazolidinones as novel P1'-ligands to enhance backbone-binding interactions with protease: synthesis, biological evaluation, and protein-ligand X-ray studies. J.Med.Chem. (2009)

Release Date

2009-06-16

Peptides

HIV-1 protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 protease

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