SMTL ID : 3kf0.1

HIV Protease with fragment 4D9 bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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: 24 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, V.32, G.48, G.49, I.50, F.53, P.81, V.82 Chain B: R.8, D.25, G.27, A.28, D.29, G.48, G.49, I.50, F.53, P.81, V.82, I.84 27 PLIP interactions: 14 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:V.32, A:F.53, A:P.81, A:P.81, A:V.82, B:F.53, B:F.53, B:P.81, B:P.81, B:P.81, B:V.82, B:I.84 Hydrogen bonds: A:R.8, A:R.8, A:D.25, A:G.27, A:D.29, A:G.48, A:G.48, B:G.27, B:D.29, B:G.48, B:G.48 Water bridges: A:G.48, A:I.50, B:R.8, B:G.48

1 x 4DX: (1S,2S)-2-methylcyclohexanol(Non-covalent)

4DX.2: 7 residues within 4Å: Chain A: K.14, I.15, G.16, G.17, L.63, I.64, E.65 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.14, A:L.63, A:E.65 Hydrogen bonds: A:I.15, A:G.17

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

DMS.3: 6 residues within 4Å: Chain A: T.12, L.19, E.65, I.66, C.67, G.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.67, A:G.68 Salt bridges: A:E.65 DMS.4: 3 residues within 4Å: Chain A: G.73, T.74, N.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.74, A:T.74, A:N.88 DMS.5: 5 residues within 4Å: Chain A: R.87, N.88, T.91 Chain B: L.5, W.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.92

2 x K: POTASSIUM ION(Non-covalent)

K.6: 3 residues within 4Å: Chain A: G.94, T.96 Chain B: N.98 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.94, A:T.96 K.8: 3 residues within 4Å: Chain A: N.98 Chain B: G.94, T.96 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:N.98, B:G.94

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

BME.7: 5 residues within 4Å: Chain B: T.12, K.14, E.65, C.67, G.68 No protein-ligand interaction detected (PLIP)

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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