SMTL ID : 4k4q.1

TL-3 inhibited Trp6Ala HIV Protease with 3-bromo-2,6-dimethoxybenzoic acid bound in flap site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NO3.1: 3 residues within 4Å: Chain A: W.42, R.57, Y.59 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.42, A:Y.59 NO3.2: 3 residues within 4Å: Chain A: F.53, I.54, K.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.55 Water bridges: A:F.53 NO3.5: 4 residues within 4Å: Chain A: D.30, K.45, T.74, L.76 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.31, A:N.88 NO3.6: 2 residues within 4Å: Chain A: K.14, G.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.14 NO3.7: 8 residues within 4Å: Chain A: T.12, I.13, K.14, L.19, E.65, I.66, C.67, G.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.67, A:G.68 NO3.9: 5 residues within 4Å: Chain B: L.19, K.20, E.21, E.34, N.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.21, B:E.34, B:N.83

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

BME.3: 3 residues within 4Å: Chain A: V.11, T.12, C.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.12, A:T.12, A:T.12

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

DMS.4: 1 residues within 4Å: Chain A: F.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.53 DMS.13: 4 residues within 4Å: Chain B: L.10, V.11, T.12, E.21 No protein-ligand interaction detected (PLIP)

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.8: 34 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, V.32, K.45, M.46, I.47, G.48, G.49, I.50, F.53, P.81, V.82, I.84 Chain B: R.8, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, G.52, T.80, P.81, V.82, I.84 Ligands: 06B.11, 06B.12 26 PLIP interactions: 15 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:A.28, A:V.32, A:I.50, A:F.53, A:P.81, A:V.82, B:A.28, B:V.32, B:P.81, B:V.82, B:I.84 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:D.29, B:G.48, B:G.48 Water bridges: A:I.50, A:I.50, B:G.48

3 x 06B: 3-bromo-2,6-dimethoxybenzoic acid(Non-covalent)

06B.10: 5 residues within 4Å: Chain B: P.44, K.45, K.55, V.56, R.57 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.44, B:K.55, B:K.55, B:K.55 Hydrogen bonds: B:K.55 Salt bridges: B:K.55 06B.11: 5 residues within 4Å: Chain A: G.48 Chain B: R.8, P.81 Ligands: 3TL.8, 06B.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.8, B:R.8 Salt bridges: B:R.8 pi-Cation interactions: B:R.8 06B.12: 5 residues within 4Å: Chain A: F.53 Chain B: R.8, P.81 Ligands: 3TL.8, 06B.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.81 Salt bridges: B:R.8

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

HIV-1 protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 protease

Related Entries With Identical Sequence