SMTL ID : 5ivt.1

Crystal Structure of HIV Protease complexed with [(1S)-1-[(S)-(4-chlorophenyl)-(3,5-difluorophenyl)methyl]-2-[[5-fluoro-4-[2-[(2R,5S)-5-(2,2,2-trifluoroethylcarbamoyloxymethyl)morpholin-4-ium-2-yl]ethyl]pyridin-1-ium-3-yl]amino]-2-oxo-ethyl]ammonium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: A.28, D.29, D.30, I.47, I.84 Ligands: 6EE.2, 6EE.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.84 Hydrogen bonds: A:D.29, A:D.30 ACT.5: 7 residues within 4Å: Chain B: A.28, D.29, D.30, I.47, G.48 Ligands: 6EE.2, 6EE.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.47 Hydrogen bonds: B:D.29, B:D.30

2 x 6EE: (betaS)-4-chloro-beta-(3,5-difluorophenyl)-N-(5-fluoro-4-{2-[(2R,5S)-5-({[(2,2,2-trifluoroethyl)carbamoyl]oxy}methyl)morpholin-2-yl]ethyl}pyridin-3-yl)-L-phenylalaninamide(Covalent)(Non-covalent)

6EE.2: 26 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, G.48, G.49, I.50, P.81, V.82, I.84 Ligands: ACT.1, 6EE.4, ACT.5 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:D.25, A:D.29, A:D.30, A:G.48, B:R.8, B:G.48 Water bridges: A:G.48, A:G.48, A:G.48, A:G.48, B:I.50, B:I.50 Hydrophobic interactions: B:L.23, B:I.50, B:P.81, B:V.82, B:V.82, B:I.84 6EE.4: 28 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, G.48, G.49, I.50, P.81, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, P.81, V.82, I.84 Ligands: ACT.1, 6EE.2, ACT.5 17 PLIP interactions: 9 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 Hydrogen bonds: A:R.8, A:G.48, B:D.25, B:D.29, B:D.30, B:G.48 Water bridges: A:I.50, A:I.50, B:G.48, B:G.48, B:G.48, B:G.48

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

CL.3: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bungard, C.J. et al., Discovery of MK-8718, an HIV Protease Inhibitor Containing a Novel Morpholine Aspartate Binding Group. Acs Med.Chem.Lett. (2016)

Release Date

2016-05-18

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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