SMTL ID : 3ebz.1

High Resolution HIV-2 Protease Structure in Complex with Clinical Drug Darunavir

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.1: 4 residues within 4Å: Chain A: L.99 Chain B: P.1 Ligands: ZN.3, CL.6 No protein-ligand interaction detected (PLIP) IMD.2: 3 residues within 4Å: Chain A: Y.14, E.65 Ligands: ZN.5 No protein-ligand interaction detected (PLIP) IMD.9: 3 residues within 4Å: Chain B: E.21 Ligands: IMD.10, ZN.13 No protein-ligand interaction detected (PLIP) IMD.10: 5 residues within 4Å: Chain B: R.8, V.10, E.21 Ligands: IMD.9, ZN.13 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.8, B:V.10 IMD.11: 9 residues within 4Å: Chain B: D.30, I.46, M.76 Ligands: ZN.14, ZN.18, CL.19, CL.20, CL.24, CL.25 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.45 IMD.12: 4 residues within 4Å: Chain B: W.6 Ligands: ZN.15, CL.22, CL.23 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:W.6

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

ZN.3: 3 residues within 4Å: Chain A: L.99 Ligands: IMD.1, CL.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.99, H2O.1, H2O.1, H2O.1 ZN.4: 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.5: 2 residues within 4Å: Chain A: E.65 Ligands: IMD.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.65, A:E.65, H2O.1 ZN.13: 3 residues within 4Å: Chain B: E.21 Ligands: IMD.9, IMD.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.21, B:E.21 ZN.14: 6 residues within 4Å: Chain B: D.30 Ligands: 017.8, IMD.11, ZN.18, CL.20, CL.25 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.30, H2O.4 ZN.15: 3 residues within 4Å: Ligands: IMD.12, CL.22, CL.23 No protein-ligand interaction detected (PLIP) ZN.16: 2 residues within 4Å: Chain B: E.65 Ligands: CL.21 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.65, H2O.5, H2O.5, H2O.5 ZN.17: 2 residues within 4Å: Chain B: E.58 Ligands: CL.24 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.58, H2O.4, H2O.8 ZN.18: 5 residues within 4Å: Chain B: D.29, D.30 Ligands: IMD.11, ZN.14, CL.25 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.30, B:D.30, H2O.4

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

CL.6: 3 residues within 4Å: Chain A: L.99 Ligands: IMD.1, ZN.3 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: K.45, I.46 Ligands: IMD.11 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain B: D.30, V.47, G.48 Ligands: 017.8, IMD.11, ZN.14 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: G.17, E.65 Ligands: ZN.16 Ligand excluded by PLIP CL.22: 7 residues within 4Å: Chain B: S.4, L.5, W.6, K.7 Ligands: IMD.12, ZN.15, CL.23 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain B: W.6, K.7 Ligands: IMD.12, ZN.15, CL.22 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: K.45, E.58 Ligands: IMD.11, ZN.17 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain B: D.29, D.30 Ligands: IMD.11, ZN.14, ZN.18 Ligand excluded by PLIP

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

NA.7: 2 residues within 4Å: Chain A: N.40, N.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.40

1 x 017: (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE(Non-covalent)

017.8: 27 residues within 4Å: Chain A: R.8, L.23, D.25, G.27, A.28, 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.14, CL.20 21 PLIP interactions: 10 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.23, B:V.47, B:I.82, A:L.23, A:A.28, A:I.32, A:P.81, A:I.82 Hydrogen bonds: B:D.25, B:G.27, B:G.27, B:D.29, B:D.30, A:D.29, A:D.30, A:D.30 Water bridges: B:I.50, A:R.8, A:I.50 Salt bridges: B:D.25, A:D.25

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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