SMTL ID : 5upz.1

HIV-1 wild Type protease with GRL-0518A , an isophthalamide-derived P2-P3 ligand with the para-hydoxymethyl sulfonamide isostere as the P2' group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-dimer

Ligands

1 x 8HD: N~3~-{(2S,3R)-3-hydroxy-4-[{[4-(hydroxymethyl)phenyl]sulfonyl}(2-methylpropyl)amino]-1-phenylbutan-2-yl}-N~1~-methyl-N~1~-[(4-methyl-1,3-oxazol-2-yl)methyl]benzene-1,3-dicarboxamide(Non-covalent)

8HD.1: 27 residues within 4Å: Chain A: 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 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, V.82, I.84 26 PLIP interactions: 15 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:V.32, A:I.47, A:I.47, A:I.50, A:P.81, A:V.82, A:V.82, A:I.84, B:L.23, B:A.28, B:V.32, B:V.82, B:I.84 Hydrogen bonds: A:D.29, A:D.30, B:D.25, B:G.27, B:G.27, B:D.29 Water bridges: A:I.50, B:I.50 Salt bridges: A:D.25, B:D.25 pi-Cation interactions: A:R.8

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

NA.2: 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

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

CL.3: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: K.45, M.46, I.47, F.53 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.45 Water bridges: A:K.45, A:K.45, A:G.48 GOL.8: 6 residues within 4Å: Chain A: T.4, L.5 Chain B: T.91, G.94, A.95, T.96 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.95, A:L.5, A:W.6 Water bridges: B:T.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Design of novel HIV-1 protease inhibitors incorporating isophthalamide-derived P2-P3 ligands: Synthesis, biological evaluation and X-ray structural studies of inhibitor-HIV-1 protease complex. Bioorg. Med. Chem. (2017)

Release Date

2017-05-10

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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