SMTL ID : 4dfg.1

Crystal Structure of Wild-type HIV-1 Protease with Cyclopentyltetrahydro- furanyl Urethanes as P2-ligand, GRL-0249A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.23 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 1 residues within 4Å: Chain A: D.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.60 Water bridges: A:R.41 NA.5: 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.6: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP

1 x 0JV: methyl N-[(3S,3aR,5R,6aR)-5-[[(2S,3R)-4-[(4-methoxyphenyl)sulfonyl-(2-methylpropyl)amino]-3-oxidanyl-1-phenyl-butan-2-yl]carbamoyloxy]-3,3a,4,5,6,6a-hexahydro-2H-cyclopenta[b]furan-3-yl]carbamate(Non-covalent)

0JV.4: 23 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, P.81, V.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, G.48, G.49, I.50, V.82 23 PLIP interactions: 9 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:A.28, A:V.32, A:P.81, A:P.81, A:V.82, B:L.23, B:V.82 Hydrogen bonds: A:D.29, A:D.30, A:I.50, B:D.25, B:G.27, B:G.27, B:D.29, B:G.48 Salt bridges: A:D.25, B:D.25 Water bridges: B:G.48, B:G.48, B:G.48, B:G.48, B:I.50, B:I.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Substituent effects on P2-cyclopentyltetrahydrofuranyl urethanes: Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors. Bioorg.Med.Chem.Lett. (2012)

Release Date

2012-03-21

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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