SMTL ID : 3kfr.1

HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

1 x 3TL: benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate(Non-covalent)

3TL.1: 27 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, M.46, I.47, 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, G.48, G.49, I.50, F.53, P.81, V.82, I.84 27 PLIP interactions: 13 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:A.28, A:I.50, A:P.81, A:P.81, A:V.82, B:A.28, B:I.50, B:F.53, B:P.81, B:V.82, B:I.84 Hydrogen bonds: A:R.8, A:G.27, A:D.29, A:D.29, A:D.29, A:G.48, A:G.48, B:D.25, B:G.27, B:D.29, B:G.48, B:G.48 Water bridges: A:R.8, B:G.48, B:I.50, B:I.50

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 3 residues within 4Å: Chain A: V.11, T.12, C.67 No protein-ligand interaction detected (PLIP) BME.4: 3 residues within 4Å: Chain B: V.11, T.12, C.67 No protein-ligand interaction detected (PLIP)

1 x 1F1: 1H-indole-6-carboxylic acid(Non-covalent)

1F1.3: 7 residues within 4Å: Chain B: W.42, P.44, K.45, M.46, K.55, V.56, R.57 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.44, B:K.55 Hydrogen bonds: B:K.45, B:V.56, B:V.56 Water bridges: B:R.57 Salt bridges: B:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perryman, A.L. et al., Fragment-based screen against HIV protease. Chem.Biol.Drug Des. (2010)

Release Date

2010-02-23

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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