SMTL ID : 3ok9.1

Crystal structure of wild-type HIV-1 protease with new oxatricyclic designed inhibitor GRL-0519A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-dimer

Ligands

1 x G52: (3R,3aS,3bR,6aS,7aS)-octahydrodifuro[2,3-b:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate(Non-covalent)

G52.1: 23 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, D.30, G.48, G.49, I.50, V.82 Chain B: R.8, D.25, G.27, A.28, D.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, I.84 19 PLIP interactions: 10 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:L.23, A:V.82, B:A.28, B:V.32, B:P.81, B:V.82, B:I.84 Hydrogen bonds: A:D.25, A:G.27, A:G.27, A:D.29, A:D.30, B:D.29, B:D.30 Water bridges: A:I.50, A:I.50 Salt bridges: A:D.25, B:R.8, B:D.25

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

NA.2: 1 residues within 4Å: Chain A: D.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.60 NA.6: 1 residues within 4Å: Chain B: D.60 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.60 Water bridges: B:P.39, B:R.41, B:R.41, B:D.60

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

CL.3: 1 residues within 4Å: Chain A: W.6 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: Q.18, M.36, S.37 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: I.47, G.48 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: K.20, E.21, N.83 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: W.42, K.55, V.56, R.57 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.55, A:R.57 Water bridges: A:K.55, A:V.56, A:V.77 GOL.11: 2 residues within 4Å: Chain B: T.4, W.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Probing Multidrug-Resistance and Protein-Ligand Interactions with Oxatricyclic Designed Ligands in HIV-1 Protease Inhibitors. Chemmedchem (2010)

Release Date

2010-09-22

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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