SMTL ID : 3vf7.1

Crystal Structure of HIV-1 Protease Mutant L76V with novel P1'-Ligands GRL-02031

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

1 x 031: (3aS,5R,6aR)-hexahydro-2H-cyclopenta[b]furan-5-yl [(1S,2R)-1-benzyl-2-hydroxy-3-([(4-methoxyphenyl)sulfonyl]{[(2R)-5-oxopyrrolidin-2-yl]methyl}amino)propyl]carbamate(Non-covalent)

031.1: 24 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, D.30, G.48, G.49, I.50, V.82 Chain B: R.8, 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: GOL.11 17 PLIP interactions: 7 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:D.25, A:G.27, A:G.27, A:D.29, A:D.30, B:G.27, B:D.29, B:D.30 Water bridges: A:I.50, B:I.50 Salt bridges: A:D.25, B:D.25 Hydrophobic interactions: B:A.28, B:V.32, B:P.81, B:V.82, B:I.84

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

NA.2: 1 residues within 4Å: Chain A: Y.59 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.38 NA.9: 1 residues within 4Å: Chain B: D.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.60, B:D.60 Water bridges: B:R.41

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

CL.3: 2 residues within 4Å: Chain A: W.6 Ligands: GOL.6 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: G.73, T.74, N.88 Ligands: GOL.5 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Q.61, Q.92 Ligands: CL.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.92 GOL.6: 3 residues within 4Å: Chain A: T.4, W.6 Ligands: CL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.4 GOL.7: 6 residues within 4Å: Chain A: T.12, I.13, E.65, I.66, A.67, G.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.12, A:K.14, A:E.65, A:G.68 Water bridges: A:T.12 GOL.8: 2 residues within 4Å: Chain A: P.39, G.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.40 Water bridges: A:L.38 GOL.11: 2 residues within 4Å: Chain B: R.8 Ligands: 031.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.8, B:R.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, Y.C. et al., Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring. J.Med.Chem. (2012)

Release Date

2012-11-21

Peptides

protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

protease

Related Entries With Identical Sequence