SMTL ID : 4tvh.1

HIV Protease (PR) dimer in closed form with TL-3 in active site and fragment AK-2097 in the outside/top of flap

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 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: 29 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, V.32, M.46, I.47, G.48, G.49, I.50, F.53, T.80, P.81, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, G.48, G.49, I.50, F.53, P.81, V.82, I.84 30 PLIP interactions: 16 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:I.50, B:F.53, B:F.53, B:P.81, B:V.82, B:I.84, A:V.32, A:I.47, A:I.50, A:F.53, A:P.81, A:P.81 Hydrogen bonds: B:R.8, B:G.27, B:D.29, B:D.30, B:G.48, B:G.48, B:I.50, A:D.25, A:G.27, A:G.27, A:D.29, A:D.29, A:G.48, A:G.48 Water bridges: B:G.48, A:I.50

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

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

1 x K97: 3-(morpholin-4-ylmethyl)-1H-indole-6-carboxylic acid(Non-covalent)

K97.3: 7 residues within 4Å: Chain B: W.42, P.44, K.45, M.46, K.55, V.56, R.57 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.44, B:K.55 Hydrogen bonds: B:K.45, B:V.56, B:V.56 Salt bridges: B:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, N. et al., Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease. J.Phys.Chem.B (2015)

Release Date

2014-09-17

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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