SMTL ID : 3qrm.1

HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-dimer

Ligands

1 x NK7: 4-{[4-(trifluoromethyl)benzyl][(3S,4S)-4-{[4-(trifluoromethyl)benzyl]amino}pyrrolidin-3-yl]sulfamoyl}benzamide(Non-covalent)

NK7.1: 28 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, L.76, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, I.84 Ligands: DTD.3 19 PLIP interactions: 13 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.23, B:A.28, B:P.81, B:V.82, B:I.84, A:A.28, A:V.32, A:I.50 Hydrogen bonds: B:D.25, B:D.29, B:D.30, B:D.30, B:D.30, B:I.50, A:D.25, A:I.50 Water bridges: B:D.29 Salt bridges: B:D.25 Halogen bonds: A:D.29

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

1 x DTD: DITHIANE DIOL(Non-covalent)

DTD.3: 9 residues within 4Å: Chain A: L.23, D.25, V.82, I.84 Chain B: G.27, G.48, G.49, I.50 Ligands: NK7.1 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.27, B:D.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lindemann, I. et al., Design of a series of novel three-armed pyrrolidine-based inhibitors for HIV-1 protease. To be Published

Release Date

2012-02-22

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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