SMTL ID : 8fui.1

HIV-1 wild type protease with GRL-02519A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyrimidin-2-amine as P2-P3 group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

1 x Y9R: N-{(2S,3R)-4-[(4-aminobenzene-1-sulfonyl)(2-methylpropyl)amino]-3-hydroxy-1-phenylbutan-2-yl}-4-methyl-3-{[(4P)-4-(pyridin-3-yl)pyrimidin-2-yl]amino}benzamide(Non-covalent)

Y9R.1: 26 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, 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, V.32, I.47, G.48, G.49, I.50, V.82, I.84 Ligands: CL.9 29 PLIP interactions: 13 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: A:A.28, A:V.32, A:I.50, A:P.81, A:V.82, A:V.82, B:L.23, B:A.28, B:D.30, B:V.32, B:I.47, B:I.47, B:V.82, B:I.84 Hydrogen bonds: A:R.8, A:R.8, A:D.30, A:D.30, B:D.25, B:G.27, B:G.27, B:D.29 Water bridges: A:D.30, B:G.48, B: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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 Water bridges: A:R.41 NA.7: 1 residues within 4Å: Chain B: D.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.60

4 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.8: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: I.47, G.48 Ligands: Y9R.1 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 2 residues within 4Å: Chain A: P.1, Q.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.1 Hydrogen bonds: A:Q.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Q.18, M.36, S.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.18, A:S.37, A:S.37

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

FMT.6: 4 residues within 4Å: Chain A: T.12, E.65, A.67, G.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.68 FMT.11: 2 residues within 4Å: Chain B: W.42, R.57 No protein-ligand interaction detected (PLIP)

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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