SMTL ID : 7wbs.1

Crystal structure of HIV-1 protease in complex with lactam derivative 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: R.8, P.81 Chain B: G.48, F.53 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:G.48, B:G.48, B:G.48 Hydrogen bonds: A:R.8, A:R.8 GOL.3: 6 residues within 4Å: Chain B: T.12, I.13, K.14, E.65, C.67, G.68 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.65, B:E.65, B:G.68 Water bridges: B:T.12

1 x 8LT: (3~{R},4~{R})-1-[(4-methoxyphenyl)methyl]-3-(3-methylbutyl)-3-[4-methylsulfonyl-2-[(2~{S})-1-oxidanylpropan-2-yl]oxy-phenyl]-4-oxidanyl-pyrrolidin-2-one(Non-covalent)

8LT.2: 24 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, 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, I.84 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:A.28, A:I.50, A:P.81, A:V.82, A:I.84, B:L.23, B:A.28, B:V.32 Hydrogen bonds: A:D.25, A:I.50, B:G.27, B:D.29, B:D.30, B:D.30, B:I.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kojima, E. et al., Pocket-to-Lead: Structure-Based De Novo Design of Novel Non-peptidic HIV-1 Protease Inhibitors Using the Ligand Binding Pocket as a Template. J.Med.Chem. (2022)

Release Date

2022-11-02

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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