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SMTL ID : 9g35.1

The HIV protease inhibitor lopinavir binding to the active site of Cryphonectria parasitica endothiapepsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x AB1: N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE(Non-covalent)

AB1.1:

20 residues within 4Å:

Chain A: D.33, D.35, G.37, I.77, S.78, Y.79, G.80, D.81, S.83, F.116, L.125, L.133, F.194, I.217, D.219, G.221, T.222, T.223, Y.226, I.304

19 PLIP interactions:

19 interactions with chain A

Hydrophobic interactions: A:I.77, A:Y.79, A:F.116, A:F.116, A:L.125, A:L.133, A:F.194, A:F.194, A:I.217, A:I.304
Hydrogen bonds: A:D.35, A:G.37, A:G.80, A:D.81, A:D.81, A:G.221, A:T.223, A:T.223
Water bridges: A:L.224

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2:

4 residues within 4Å:

Chain A: D.15, L.224, F.280, F.291

2 PLIP interactions:

2 interactions with chain A

Hydrogen bonds: A:Y.226, A:I.283

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3:	6 residues within 4Å: Chain A: F.253, A.257, T.258, L.259, D.276, D.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.255, A:L.259 Water bridges: A:L.259, A:D.276
EDO.5:	3 residues within 4Å: Chain A: S.154, V.156, I.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.154 Water bridges: A:I.174

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4:	4 residues within 4Å: Chain A: T.2, S.4, F.173, D.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.2, A:T.2, A:S.4 Water bridges: A:D.175, A:D.175
PG4.6:	8 residues within 4Å: Chain A: A.187, V.188, S.189, K.191, E.196, W.197, T.198, D.215 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.189, A:K.191, A:K.191 Water bridges: A:T.198

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Falke, S. et al., The HIV protease inhibitor lopinavir binding to the active site of Cryphonectria parasitica endothiapepsin. To Be Published

Release Date

2024-07-24

Peptides

Endothiapepsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Endothiapepsin

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