SMTL ID : 5w5w.1

HIV Protease (PR) in open form with Mg2+ in active site and HIVE-9 in eye site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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: 31 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, 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, I.47, G.48, G.49, I.50, F.53, P.81, V.82, I.84 28 PLIP interactions: 17 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:V.32, A:I.50, A:F.53, A:P.81, A:P.81, A:V.82, A:I.84, B:A.28, B:I.47, B:F.53, 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:D.29, A:G.48, A:G.48, B:R.8, B:D.29, B:G.48, B:G.48, B:G.48

1 x HV9: 4-methyl-N-({1-[4-(trifluoromethyl)pyrimidin-2-yl]piperidin-4-yl}carbamoyl)benzene-1-sulfonamide(Non-covalent)

HV9.2: 6 residues within 4Å: Chain A: P.1, Q.2, I.3, V.11, T.12, A.67 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.3, A:A.67 Hydrogen bonds: A:Q.2, A:Q.2, A:Q.2 Halogen bonds: A:T.12

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

DMS.3: 3 residues within 4Å: Chain B: I.54, K.55, P.79 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

2018-06-20

Peptides

HIV-1 protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 protease

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