SMTL ID : 6c8x.1

Wild-type HIV-1 protease in complex with a phenylboronic acid (P2') analog of darunavir

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

1 x BVR: [4-[[(2~{R},3~{S})-3-[[(3~{a}~{S},4~{R},6~{a}~{R})-2,3,3~{a},4,5,6~{a}-hexahydrofuro[2,3-b]furan-4-yl]oxycarbonylamino]-2-oxidanyl-4-phenyl-butyl]-(2-methylpropyl)sulfamoyl]phenyl]-oxidanyl-oxidanylidene-boron(Non-covalent)

BVR.1: 24 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, V.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, V.82 20 PLIP interactions: 11 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:V.32, A:V.82, A:I.84, B:L.23, B:V.82 Hydrogen bonds: A:D.30, B:D.25, B:G.27, B:G.27, B:D.29, B:D.30 Water bridges: A:D.29, A:G.48, A:G.48, A:I.50, B:I.50 Salt bridges: A:D.25, B:D.25

2 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.3: 2 residues within 4Å: Chain B: W.42, P.44 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain B: T.12, E.65, A.67, G.68 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.65, B:G.68 Water bridges: B:T.12, B:T.12, B:E.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Windsor, I.W. et al., Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid. J. Am. Chem. Soc. (2018)

Release Date

2018-12-05

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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