SMTL ID : 3vfa.1

Crystal Structure of HIV-1 Protease Mutant V82A with novel P1'-Ligands GRL-02031

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 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: 23 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, G.48, G.49, I.50, A.82 Ligands: CL.5 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.28, A:V.32, A:P.81, A:I.84 Hydrogen bonds: A:G.27, A:D.29, A:D.30, B:D.25, B:G.27, B:D.29 Salt bridges: A:D.25, B:D.25 Water bridges: B:I.50, B:I.50

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

NA.2: 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

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

CL.3: 3 residues within 4Å: Chain A: G.73, T.74, N.88 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: Q.18, M.36, S.37 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: I.47, G.48 Ligands: 031.1 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: I.54, K.55 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: V.11, T.12, A.67 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: K.20, E.21, N.83 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: I.54, K.55 Ligand excluded by PLIP

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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