SMTL ID : 3mxd.1

Crystal structure of HIV-1 protease inhibitor KC53 in complex with wild-type protease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

1 x K53: (5S)-N-{(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-1-benzyl-2-hydroxypropyl}-3-(2-hydroxyphenyl)-2 -oxo-1,3-oxazolidine-5-carboxamide(Non-covalent)

K53.1: 25 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, V.82 Chain B: R.8, 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 20 PLIP interactions: 9 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:A.28, B:V.32, B:P.81, B:V.82, B:I.84, A:L.23, A:I.47, A:V.82 Hydrogen bonds: B:D.29, B:D.30, A:D.25, A:G.27, A:D.29, A:D.30, A:D.30 Water bridges: B:G.48, A:I.50, A:I.50 Salt bridges: B:D.25, A:D.25

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: R.14, G.16, G.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.17 Water bridges: A:G.16, A:G.16 Salt bridges: A:R.14 PO4.3: 2 residues within 4Å: Chain A: K.7, R.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.8 PO4.5: 1 residues within 4Å: Chain B: P.1 No protein-ligand interaction detected (PLIP) PO4.6: 2 residues within 4Å: Chain B: P.39, G.40 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.40

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

ACT.4: 3 residues within 4Å: Chain A: K.20, E.21, N.83 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.21, A:N.83 Water bridges: A:E.34 Salt bridges: A:K.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ali, A. et al., Structure-Based Design, Synthesis, and Structure-Activity Relationship Studies of HIV-1 Protease Inhibitors Incorporating Phenyloxazolidinones. J.Med.Chem. (2010)

Release Date

2010-11-10

Peptides

HIV-1 protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 protease

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