SMTL ID : 5yok.1

Structure of HIV-1 Protease in Complex with Inhibitor KNI-1657

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.85 Å

Oligo State

homo-dimer

Ligands

1 x 8Z0: (4R)-N-[(2,6-dimethylphenyl)methyl]-3-[(2S,3S)-3-[[(2S)-2-[(7-methoxy-1-benzofuran-2-yl)carbonylamino]-2-[(3R)-oxolan-3 -yl]ethanoyl]amino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide(Non-covalent)

8Z0.1: 35 residues within 4Å: Chain A: R.9, L.24, D.26, G.28, A.29, D.30, D.31, T.32, V.33, I.48, G.49, G.50, I.51, F.54, L.77, P.82, V.83, I.85 Chain B: R.9, L.24, D.26, G.28, A.29, D.30, D.31, T.32, V.33, I.48, G.49, G.50, I.51, L.77, P.82, V.83, I.85 20 PLIP interactions: 11 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.29, B:D.31, B:V.33, B:I.48, B:I.48, B:V.83, B:I.85, A:L.24, A:A.29, A:I.51 Hydrogen bonds: B:D.26, B:I.51, A:G.28, A:G.28, A:D.30, A:D.31, A:G.49 Water bridges: B:R.9, B:G.28, A:G.49

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain B: T.13, I.14, K.15, L.20, E.66, A.68, G.69 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.13, B:E.66, B:G.69 GOL.3: 8 residues within 4Å: Chain B: E.36, W.43, K.56, V.57, R.58, V.78, G.79, P.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.58, B:V.78 Water bridges: B:V.57, B:V.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hidaka, K. et al., Identification of Highly Potent Human Immunodeficiency Virus Type-1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine. J. Med. Chem. (2018)

Release Date

2018-07-18

Peptides

HIV-1 PROTEASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 PROTEASE