SMTL ID : 3vf5.1

Crystal Structure of HIV-1 Protease Mutant I47V with novel P1'-Ligands GRL-02031

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 1 residues within 4Å: Chain A: D.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.60, A:D.60 Water bridges: A:R.41 NA.7: 1 residues within 4Å: Chain B: D.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.60, B:D.60

4 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: 3 residues within 4Å: Chain A: V.47, G.48 Ligands: 031.6 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: G.40, R.41, W.42 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.42 Hydrogen bonds: A:W.42, A:W.42 ACT.5: 5 residues within 4Å: Chain A: W.42, P.44, K.55, V.56, R.57 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.55, A:R.57 Hydrogen bonds: A:V.56 Salt bridges: A:K.55

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)

031.6: 26 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, P.81, V.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, V.47, G.48, G.49, I.50, P.81, V.82, I.84 Ligands: CL.3 20 PLIP interactions: 9 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:V.47, B:I.84, A:A.28, A:V.32, A:P.81, A:V.82, A:I.84 Hydrogen bonds: B:D.25, B:G.27, B:G.27, B:D.29, A:G.27, A:D.29, A:D.30 Water bridges: B:I.50, B:I.50, A:I.50, A:I.50 Salt bridges: B:D.25, A:D.25

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: T.4, L.5, W.6 Chain B: T.91, G.94, A.95, T.96 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.5, B:A.95

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