SMTL ID : 3kdc.1

Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10074

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

1 x JZP: (4R)-3-[(2S,3S)-3-{[(2,6-dichlorophenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide(Non-covalent)

JZP.1: 26 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, V.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, V.82, I.84 21 PLIP interactions: 11 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:A.28, A:D.30, A:V.32, A:I.47, A:P.81, A:V.82, A:I.84, B:L.23, B:D.29, B:I.47, B:I.50, B:V.82, B:I.84 Hydrogen bonds: A:G.27, A:G.27, A:D.29, B:D.25, B:G.27, B:D.29 Water bridges: A:I.50, B:I.50

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: Q.18, M.36, S.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.18, A:S.37, A:S.37

4 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: 6 residues within 4Å: Chain A: G.49, I.50, G.51, G.52 Chain B: I.54, P.79 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: G.73, T.74, N.88 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain B: W.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawasaki, Y. et al., How much binding affinity can be gained by filling a cavity?. Chem.Biol.Drug Des. (2010)

Release Date

2010-03-16

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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