SMTL ID : 8fuj.1

HIV-1 wild type protease with GRL-03419A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyrimidin-2-amine as P2-P3 group and 3,5-difluorophenylmethyl as the P1 group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

homo-dimer

Ligands

1 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

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.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 CL.8: 4 residues within 4Å: Chain B: T.4, L.5, W.6, K.7 Ligand excluded by PLIP

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 3 residues within 4Å: Chain A: T.4, W.6, K.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.4, A:K.7 FMT.4: 2 residues within 4Å: Chain A: G.52, F.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.53, A:F.53

1 x Y9N: N-{(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-[(4-methoxybenzene-1-sulfonyl)(2-methylpropyl)amino]butan-2-yl}-4-methyl-3-{[(4M)-4-(pyridin-3-yl)pyrimidin-2-yl]amino}benzamide(Non-covalent)

Y9N.5: 26 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, V.32, 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, M.46, I.47, G.48, G.49, I.50, F.53, V.82, I.84 21 PLIP interactions: 12 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:D.30, B:I.47, B:V.82, B:I.84, A:A.28, A:V.32, A:I.50, A:V.82, A:I.84 Hydrogen bonds: B:G.27, B:G.27, B:G.48, B:G.48, A:D.29, A:D.30 Water bridges: B:D.29, B:I.50, A:I.50 Salt bridges: A:D.25

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain B: T.12, E.65, A.67, G.68 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.65, B:G.68 Water bridges: B:T.12, B:T.12, B:T.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation. Eur.J.Med.Chem. (2023)

Release Date

2023-05-24

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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