SMTL ID : 6b3h.1

Crystal Structure of HIV Protease complexed with N-(2-(2-((6R,9S)-2,2-dioxido-2-thia-1,7-diazabicyclo[4.3.1]decan-9-yl)ethyl)-3-fluorophenyl)-3,3-bis(4-fluorophenyl)propanamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

2 x CN4: N-(2-{2-[(6R,9S)-2,2-dioxo-2lambda~6~-thia-1,7-diazabicyclo[4.3.1]decan-9-yl]ethyl}-3-fluorophenyl)-3,3-bis(4-fluorophenyl)propanamide(Non-covalent)

CN4.1: 15 residues within 4Å: Chain A: G.27, D.29, D.30, V.32, K.45, I.47, G.48, G.49, L.76 Chain B: R.8, L.23, P.81, V.82, I.84 Ligands: CN4.3 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.23, B:P.81, B:V.82, B:V.82, A:D.29, A:V.32, A:I.47 Hydrogen bonds: B:R.8, A:D.29, A:K.45, A:G.48, A:G.48 Salt bridges: A:D.29 Halogen bonds: A:D.30 CN4.3: 22 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, G.49, I.50, P.81, V.82, I.84 Chain B: D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, I.84 Ligands: CN4.1 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.23, A:P.81, A:V.82, A:V.82, A:I.84, B:V.32, B:I.47 Hydrogen bonds: A:I.50, B:D.25, B:D.29, B:G.48, B:I.50 Salt bridges: A:D.25, B:D.25 pi-Cation interactions: A:R.8 Water bridges: B:G.48

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: V.11, T.12, C.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bungard, C.J. et al., Design and Synthesis of Piperazine Sulfonamide Cores Leading to Highly Potent HIV-1 Protease Inhibitors. ACS Med Chem Lett (2017)

Release Date

2018-01-03

Peptides

HIV-1 Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 Protease

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