SMTL ID : 4yhq.1

Crystal structure of multidrug resistant clinical isolate PR20 with GRL-5010A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

1 x G10: (3R,3aS,6aS)-4,4-difluorohexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[(4-aminophenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate(Non-covalent)

G10.1: 26 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, I.50, V.82 Chain B: L.23, D.25, G.27, A.28, D.29, N.30, I.32, V.47, G.48, G.49, I.50, P.81, V.82, V.84 28 PLIP interactions: 11 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:L.23, A:V.47, A:I.50, A:V.82, B:L.23, B:A.28, B:I.32, B:V.47, B:I.50, B:P.81, B:P.81, B:V.82, B:V.84 Hydrogen bonds: A:D.25, A:G.27, A:G.27, A:D.29, A:N.30, A:I.50, B:D.29, B:N.30, B:N.30 Salt bridges: A:D.25, B:D.25 Water bridges: B:I.50, B:I.50, B:I.50, B:I.50

4 x Y1: YTTRIUM ION(Non-covalent)

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

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

CL.4: 5 residues within 4Å: Chain A: E.34, D.35 Ligands: Y1.2, Y1.3, CL.5 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: D.35 Ligands: Y1.2, Y1.3, CL.4 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: K.7, R.8 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: K.7, R.8 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain A: G.73, T.74, D.88, T.89, Q.92 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.74, A:T.74, A:Q.92 Water bridges: A:D.88

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: P.39, G.40, Q.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.39 GOL.13: 4 residues within 4Å: Chain A: W.6 Chain B: R.87, D.88, T.91 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.87, B:R.87, A:W.6

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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