SMTL ID : 5vea.1

HIV Protease (PR) with TL-3 in active site and 4-methylbenzene-1,2-diamine in exosite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 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: 18 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, M.46, I.47, G.48, G.49, I.50, I.84 Chain B: R.8, D.25, I.50, P.81, V.82, I.84 Ligands: 3TL.6 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:I.50, B:P.81, B:V.82, A:I.50, A:I.84 Hydrogen bonds: B:D.25, A:G.27, A:D.29, A:D.29, A:G.48, A:G.48 Water bridges: B:I.50, B:I.50, A:I.50, A:I.50 pi-Stacking: A:F.53 3TL.6: 18 residues within 4Å: Chain A: R.8, D.25, I.50, P.81, V.82, I.84 Chain B: D.25, G.27, A.28, D.29, D.30, M.46, I.47, G.48, G.49, I.50, I.84 Ligands: 3TL.1 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:I.50, A:P.81, A:V.82, B:I.50, B:I.84 Hydrogen bonds: A:D.25, B:G.27, B:D.29, B:D.29, B:D.29, B:G.48, B:G.48 Water bridges: A:I.50, A:I.50, B:I.50, B:I.50 pi-Stacking: B:F.53

2 x 9AY: 4-methylbenzene-1,2-diamine(Non-covalent)

9AY.2: 5 residues within 4Å: Chain A: P.39, D.60, Q.61, I.62 Ligands: DMS.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.39, A:P.39, A:I.62 Hydrogen bonds: A:Q.61, A:Q.61 Water bridges: A:D.60 9AY.7: 5 residues within 4Å: Chain B: P.39, D.60, Q.61, I.62 Ligands: DMS.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.39, B:P.39, B:I.62 Hydrogen bonds: B:Q.61, B:Q.61 Water bridges: B:D.60

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

DMS.3: 8 residues within 4Å: Chain A: T.12, I.13, K.14, L.19, E.65, I.66, C.67, G.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.14, A:G.68 Salt bridges: A:E.65 DMS.4: 6 residues within 4Å: Chain A: L.38, P.39, Q.61, I.62, L.63 Ligands: 9AY.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.16 DMS.5: 3 residues within 4Å: Chain A: P.44, K.45, M.46 No protein-ligand interaction detected (PLIP) DMS.8: 8 residues within 4Å: Chain B: T.12, I.13, K.14, L.19, E.65, I.66, C.67, G.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.14, B:G.68 Salt bridges: B:E.65 DMS.9: 6 residues within 4Å: Chain B: L.38, P.39, Q.61, I.62, L.63 Ligands: 9AY.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.16 DMS.10: 3 residues within 4Å: Chain B: P.44, K.45, M.46 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Forli, S. et al., Fragment-based campaign for the identification of potential exosite binders of HIV-1 Protease. to be published

Release Date

2018-04-25

Peptides

HIV-1 protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HIV-1 protease

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