SMTL ID : 3bc4.1

I84V HIV-1 protease in complex with a pyrrolidine diester

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

4 x LLG: 2-aminoethyl naphthalen-1-ylacetate(Non-covalent)

LLG.1: 13 residues within 4Å: Chain A: D.25, G.27, A.28, T.80, P.81, V.82, V.84 Chain B: D.25, G.27, I.50 Ligands: LLG.2, LLG.4, LLG.5 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.50, B:I.50, A:P.81, A:V.82, A:V.84 Hydrogen bonds: B:D.25 LLG.2: 10 residues within 4Å: Chain A: I.47, G.48, I.50, G.51, G.52, F.53, I.54 Ligands: LLG.1, LLG.4, LLG.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:G.51 Hydrophobic interactions: A:I.54 LLG.4: 13 residues within 4Å: Chain A: D.25, G.27, I.50 Chain B: D.25, G.27, A.28, T.80, P.81, V.82, V.84 Ligands: LLG.1, LLG.2, LLG.5 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.50, A:I.50, B:P.81, B:V.82, B:V.84 Hydrogen bonds: A:D.25 LLG.5: 10 residues within 4Å: Chain B: I.47, G.48, I.50, G.51, G.52, F.53, I.54 Ligands: LLG.1, LLG.2, LLG.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:G.51 Hydrophobic interactions: B:I.54

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 2 residues within 4Å: Chain A: G.52, F.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.53 DMS.6: 2 residues within 4Å: Chain B: G.52, F.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blum, A. et al., Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors. Chemmedchem (2008)

Release Date

2008-09-02

Peptides

protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

protease

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