SMTL ID : 4djo.1

Crystal Structure of wild-type HIV-1 Protease in Complex with MKP56

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

1 x MK5: 2-[(dichloroacetyl)amino]ethyl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl][(2S)-2-methylbutyl]amino}-1-phenylbutan-2-yl]carbamate(Non-covalent)

MK5.1: 24 residues within 4Å: Chain A: D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, P.81, I.84 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 18 PLIP interactions: 9 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:P.81, B:A.28, B:V.32, B:I.50, B:P.81, B:V.82 Hydrogen bonds: A:D.25, A:G.27, A:G.27, A:D.29, A:D.30, A:G.48, B:D.29, B:D.30 Water bridges: A:I.50, B:I.50 Salt bridges: A:D.25, B:D.25

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: K.7, R.8 Chain B: R.87 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.8, B:R.87, B:R.87

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

ACT.3: 3 residues within 4Å: Chain A: K.20, E.21, N.83 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.21 Hydrogen bonds: A:E.21, A:E.21, A:N.83 Water bridges: A:E.34, A:E.34 Salt bridges: A:K.20

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 1 residues within 4Å: Chain B: P.1 No protein-ligand interaction detected (PLIP) PO4.5: 2 residues within 4Å: Chain B: P.39, G.40 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parai, M.K. et al., Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. J.Med.Chem. (2012)

Release Date

2012-08-01

Peptides

Pol polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pol polyprotein

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