SMTL ID : 4zip.1

HIV-1 wild Type protease with GRL-0648A (a isophthalamide-derived P2-Ligand)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.11 Å

Oligo State

homo-dimer

Ligands

3 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 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 NA.6: 1 residues within 4Å: Chain B: Y.59 No protein-ligand interaction detected (PLIP)

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.7: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.8: 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: 7 residues within 4Å: Chain A: T.4, L.5, W.6 Chain B: T.91, G.94, A.95, T.96 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:T.91 Hydrogen bonds: A:T.4, A:L.5, A:W.6

1 x G64: N-[(2,5-dimethyl-1,3-oxazol-4-yl)methyl]-N'-[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]-N,5-dimethylbenzene-1,3-dicarboxamide(Non-covalent)

G64.4: 27 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, 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, V.82, I.84 23 PLIP interactions: 12 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:V.32, B:I.47, B:V.82, B:I.84, A:A.28, A:V.32, A:I.50, A:P.81, A:P.81, A:V.82, A:I.84 Hydrogen bonds: B:D.25, B:G.27, B:G.27, B:D.29, A:D.29, A:D.30 Water bridges: B:I.50, A:I.50 Salt bridges: B:D.25, A:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Structure-based design, synthesis, X-ray studies, and biological evaluation of novel HIV-1 protease inhibitors containing isophthalamide-derived P2-ligands. Bioorg.Med.Chem.Lett. (2015)

Release Date

2015-07-15

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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