SMTL ID : 2q5k.1

Crystal structure of lopinavir bound to wild type HIV-1 protease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 2 residues within 4Å: Chain A: K.7, R.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:R.87, A:R.8 Hydrogen bonds: A:R.8 PO4.2: 3 residues within 4Å: Chain A: G.68, H.69, K.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.70, A:K.70 PO4.3: 1 residues within 4Å: Chain A: C.67 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.12 PO4.5: 4 residues within 4Å: Chain B: L.19, K.20, E.21, N.83 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.21, B:N.83 Water bridges: B:E.34, B:N.83 Salt bridges: B:K.20

1 x AB1: N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE(Non-covalent)

AB1.4: 24 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, V.32, G.48, G.49, I.50, P.81, V.82, I.84 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 22 PLIP interactions: 13 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.28, B:D.29, B:D.30, B:V.32, B:I.47, B:I.50, B:P.81, B:V.82, A:A.28, A:V.32, A:P.81, A:P.81, A:V.82, A:I.84 Hydrogen bonds: B:R.8, B:D.25, B:G.27, A:G.27, A:D.29, A:D.29 Water bridges: B:R.8, B:I.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reddy, G.S. et al., Design and Synthesis of HIV-1 Protease Inhibitors Incorporating Oxazolidinones as P2/P2' Ligands in Pseudosymmetric Dipeptide Isosteres. J.Med.Chem. (2007)

Release Date

2007-09-04

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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