SMTL ID : 3ecg.1

High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-98065

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.18 Å

Oligo State

homo-dimer

Ligands

1 x 065: (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(2S,3R)-3-HYDROXY-4-(N-ISOBUTYLBENZO[D][1,3]DIOXOLE-5-SULFONAMIDO)-1-PHENYLBUTAN-2-YLCARBAMATE(Non-covalent)

065.1: 28 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, D.30, I.32, G.48, G.49, I.50, P.81, I.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, I.32, V.47, G.48, G.49, I.50, I.82 Ligands: ZN.4, ZN.18, CL.24 22 PLIP interactions: 10 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:L.23, A:A.28, A:I.32, A:P.81, A:I.82, B:L.23, B:V.47, B:I.82 Hydrogen bonds: A:D.29, A:D.30, B:D.25, B:G.27, B:G.27, B:D.29, B:D.30, B:D.30 Water bridges: A:G.48, A:I.50, B:D.29, B:I.50 Salt bridges: A:D.25, B:D.25

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 4 residues within 4Å: Chain A: L.99 Chain B: P.1 Ligands: ZN.5, CL.11 No protein-ligand interaction detected (PLIP) IMD.3: 3 residues within 4Å: Chain A: Y.14, E.65 Ligands: ZN.7 No protein-ligand interaction detected (PLIP) IMD.13: 3 residues within 4Å: Chain B: E.21 Ligands: IMD.14, ZN.17 No protein-ligand interaction detected (PLIP) IMD.14: 5 residues within 4Å: Chain B: R.8, V.10, E.21 Ligands: IMD.13, ZN.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.8 IMD.15: 7 residues within 4Å: Chain B: D.30, I.46, M.76 Ligands: ZN.18, ZN.22, CL.23, CL.24 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.45 IMD.16: 5 residues within 4Å: Chain B: W.6 Ligands: ZN.19, CL.26, CL.27, CL.28 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:W.6

11 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.4: 3 residues within 4Å: Chain A: D.30 Ligands: 065.1, CL.9 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.30, H2O.1, H2O.1, H2O.1 ZN.5: 3 residues within 4Å: Chain A: L.99 Ligands: IMD.2, CL.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.99, H2O.1, H2O.1 ZN.6: 1 residues within 4Å: Chain A: D.79 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.79, A:D.79, H2O.1, H2O.1 ZN.7: 2 residues within 4Å: Chain A: E.65 Ligands: IMD.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.65, H2O.1 ZN.8: 2 residues within 4Å: Chain A: E.63 Ligands: CL.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.63, H2O.1 ZN.17: 3 residues within 4Å: Chain B: E.21 Ligands: IMD.13, IMD.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.21, B:E.21 ZN.18: 5 residues within 4Å: Chain B: D.30 Ligands: 065.1, IMD.15, ZN.22, CL.24 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.30, H2O.4 ZN.19: 4 residues within 4Å: Ligands: IMD.16, CL.26, CL.27, CL.28 No protein-ligand interaction detected (PLIP) ZN.20: 2 residues within 4Å: Chain B: E.65 Ligands: CL.25 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.65, H2O.4, H2O.4 ZN.21: 1 residues within 4Å: Chain B: E.58 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, H2O.4, H2O.7 ZN.22: 4 residues within 4Å: Chain B: D.29, D.30 Ligands: IMD.15, ZN.18 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.30, B:D.30, H2O.4, H2O.4

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

CL.9: 2 residues within 4Å: Chain A: D.30 Ligands: ZN.4 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: E.63, K.70 Ligands: ZN.8 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: L.99 Ligands: IMD.2, ZN.5 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: K.45, I.46 Ligands: IMD.15 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain B: V.47, G.48 Ligands: 065.1, IMD.15, ZN.18 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain B: G.17, E.65 Ligands: ZN.20 Ligand excluded by PLIP CL.26: 8 residues within 4Å: Chain B: S.4, L.5, W.6, K.7 Ligands: IMD.16, ZN.19, CL.27, CL.28 Ligand excluded by PLIP CL.27: 6 residues within 4Å: Chain B: W.6, K.7 Ligands: IMD.16, ZN.19, CL.26, CL.28 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain B: K.7 Ligands: IMD.16, ZN.19, CL.26, CL.27 Ligand excluded by PLIP

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

NA.12: 2 residues within 4Å: Chain A: N.40, N.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalevsky, A.Y. et al., Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease. J.Mol.Biol. (2008)

Release Date

2008-09-16

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protease

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