SMTL ID : 4ye3.1

Crystal Structure of Multidrug Resistant HIV-1 Protease Clinical Isolate PR20 with Inhibitor GRL-4410A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

4 x Y1: YTTRIUM ION(Non-covalent)

Y1.1: 5 residues within 4Å: Chain A: E.34, D.35 Ligands: Y1.2, CL.3, CL.4 No protein-ligand interaction detected (PLIP) Y1.2: 5 residues within 4Å: Chain A: E.34, D.35 Ligands: Y1.1, CL.3, CL.4 No protein-ligand interaction detected (PLIP) Y1.9: 5 residues within 4Å: Chain B: E.58, D.60 Ligands: Y1.10, CL.11, CL.12 No protein-ligand interaction detected (PLIP) Y1.10: 5 residues within 4Å: Chain B: E.58, D.60 Ligands: Y1.9, CL.11, CL.12 No protein-ligand interaction detected (PLIP)

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

CL.3: 4 residues within 4Å: Chain A: E.34, D.35 Ligands: Y1.1, Y1.2 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: E.34, D.35 Ligands: Y1.1, Y1.2 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.7, R.8 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: E.58 Ligands: Y1.9, Y1.10 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: E.58, D.60 Ligands: Y1.9, Y1.10 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: W.6 Chain B: R.87, D.88, T.91 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.87, B:R.87, B:R.87, B:T.91 GOL.7: 3 residues within 4Å: Chain A: R.87, D.88 Chain B: W.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.87, A:R.87

1 x G04: (3R,3aS,4R,6aR)-4-methoxyhexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate(Non-covalent)

G04.8: 23 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, N.30, I.32, V.47, G.48, G.49, P.81, V.82 Chain B: L.23, D.25, G.27, A.28, D.29, N.30, I.32, G.48, G.49, I.50, V.82 19 PLIP interactions: 9 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:I.32, A:P.81, A:V.82, B:L.23, B:V.82 Hydrogen bonds: A:D.29, A:N.30, A:I.50, B:D.25, B:G.27, B:G.27, B:D.29, B:N.30, B:I.50 Salt bridges: A:D.25, B:D.25 Water bridges: B:G.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agniswamy, J. et al., Substituted Bis-THF Protease Inhibitors with Improved Potency against Highly Resistant Mature HIV-1 Protease PR20. J.Med.Chem. (2015)

Release Date

2015-06-10

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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