SMTL ID : 3vfb.1

Crystal Structure of HIV-1 Protease Mutant N88D with novel P1'-Ligands GRL-02031

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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: 25 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, I.47, G.48, G.49, I.50, P.81, V.82, I.84 Ligands: CL.7 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.28, B:V.32, B:P.81, B:V.82, B:I.84 Hydrogen bonds: B:G.27, B:D.29, B:D.30, B:D.30, A:D.25, A:G.27, A:G.27, A:D.29 Water bridges: B:I.50, A:I.50 Salt bridges: B:D.25, A:D.25

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

CL.2: 2 residues within 4Å: Chain A: W.6 Ligands: GOL.5 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: I.47, G.48 Ligands: 031.1 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: T.12, I.13, K.14, E.65, I.66, A.67, G.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.12, A:E.65, A:A.67, A:G.68 Water bridges: A:T.12 GOL.4: 4 residues within 4Å: Chain A: W.42, K.55, V.56, R.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.55, A:R.57 Water bridges: A:V.56 GOL.5: 3 residues within 4Å: Chain A: T.4, W.6 Ligands: CL.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.4

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

NA.6: 1 residues within 4Å: Chain B: D.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.60 Water bridges: B:R.41

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

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