SMTL ID : 3i6o.1

Crystal structure of wild type HIV-1 protease with macrocyclic inhibitor GRL-0216A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.17 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.11: 1 residues within 4Å: Chain B: D.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.60

19 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 2 residues within 4Å: Chain A: T.74, N.88 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: G.48 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: T.12, E.65, A.67, G.68 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: T.12, A.67 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: Q.61 Ligands: IOD.7 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Ligands: IOD.6 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: I.54, K.55 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: I.63 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain B: T.12 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain B: K.55 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain B: K.55 Ligands: IOD.15 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain B: P.44, K.55 Ligands: IOD.14 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain B: G.48 Ligands: GR6.23 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain B: P.39, I.63 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain B: G.40 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain B: K.7, R.8 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain B: T.12, E.65, G.68 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain B: I.72 Ligands: IOD.22 Ligand excluded by PLIP IOD.22: 1 residues within 4Å: Ligands: IOD.21 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: K.14, I.15, G.16, G.17, I.63, I.64, E.65 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.17, A:I.63, A:E.65 Water bridges: A:G.16, A:G.16 GOL.24: 6 residues within 4Å: Chain A: L.5, W.6 Chain B: D.29, R.87, N.88, T.91 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.30, B:D.30, B:T.91, B:T.91, A:W.6

1 x GR6: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-1-benzyl-2-hydroxy-3-[(7E)-13-methoxy-1,1-dioxido-3,4,5,6,9,10-hexahydro-2H-11,1,2-benzoxathiazacyclotridecin-2-yl]propyl}carbamate(Non-covalent)

GR6.23: 27 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, G.48, G.49, I.50, P.81, V.82, I.84 Chain B: R.8, L.23, D.25, G.27, A.28, D.29, D.30, V.32, G.48, G.49, I.50, P.81, V.82, I.84 Ligands: IOD.16 24 PLIP interactions: 12 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:P.81, A:V.82, A:V.82, A:I.84, B:L.23, B:A.28, B:V.32, B:I.50, B:P.81, B:P.81, B:V.82, B:I.84 Hydrogen bonds: A:D.25, A:G.27, A:G.27, A:D.29, A:D.30, B:D.29, B:D.30, B:I.50 Water bridges: A:I.50, A:I.50 Salt bridges: A:D.25, B:D.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, A.K. et al., Design, Synthesis, Protein-Ligand X-ray Structure, and Biological Evaluation of a Series of Novel Macrocyclic Human Immunodeficiency Virus-1 Protease Inhibitors to Combat Drug Resistance. J.Med.Chem. (2009)

Release Date

2009-09-29

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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