SMTL ID : 4k4r.1

TL-3 inhibited Trp6Ala HIV Protease with 1-bromo-2-napthoic acid bound in exosite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

DMS.1: 7 residues within 4Å: Chain A: T.12, I.13, K.14, E.65, I.66, C.67, G.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.68 Salt bridges: A:E.65

2 x 27B: 1-bromonaphthalene-2-carboxylic acid(Non-covalent)

27B.2: 6 residues within 4Å: Chain A: K.14, L.63, I.64, E.65, K.70, A.71 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.63, A:K.70, A:K.70, A:K.70 Hydrogen bonds: A:E.65 Salt bridges: A:K.14 Halogen bonds: A:K.14 27B.8: 1 residues within 4Å: Chain B: K.14 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.14

5 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 7 residues within 4Å: Chain A: E.35, K.55, V.56, R.57, V.77, G.78, P.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.35, A:R.57, A:R.57 NO3.4: 1 residues within 4Å: Chain A: F.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.53 Water bridges: A:F.53 NO3.5: 3 residues within 4Å: Chain A: F.53, I.54, K.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.55 NO3.7: 7 residues within 4Å: Chain B: T.12, I.13, K.14, E.65, I.66, C.67, G.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.13, B:C.67, B:G.68 NO3.9: 4 residues within 4Å: Chain B: L.19, K.20, E.21, N.83 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.20, B:K.20, B:E.21, B:N.83

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.6: 26 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, V.32, 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, P.81, I.84 25 PLIP interactions: 14 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:A.28, A:V.32, A:I.50, A:I.50, A:P.81, A:V.82, B:A.28, B:I.50, B:P.81 Hydrogen bonds: A:R.8, A:D.25, A:G.27, A:D.29, A:D.29, A:G.48, A:G.48, B:D.25, B:G.27, B:G.27, B:D.29, B:G.48, B:G.48, B:G.48 Water bridges: A:I.50, B:I.50

1 x BR: BROMIDE ION(Non-covalent)

BR.10: 3 residues within 4Å: Chain B: P.44, K.45, M.46 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tiefenbrunn, T. et al., Crystallographic Fragment-Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease. Chem.Biol.Drug Des. (2014)

Release Date

2013-09-18

Peptides

Gag-Pol polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gag-Pol polyprotein

Related Entries With Identical Sequence