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SMTL ID : 3psy.1

Endothiapepsin in complex with an inhibitor based on the Gewald reaction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x RB9: N-benzyl-2-({N-[2-(1H-indol-3-yl)ethyl]glycyl}amino)-4-phenylthiophene-3-carboxamide(Non-covalent)

RB9.1:

22 residues within 4Å:

Chain A: D.33, D.35, G.37, Y.79, G.80, D.81, S.83, F.116, D.119, I.122, L.125, F.194, I.217, D.219, G.221, T.222, Y.226, I.300, I.302, I.304
Ligands: DMS.2, PG4.4

14 PLIP interactions:

14 interactions with chain A

Hydrophobic interactions: A:Y.79, A:D.81, A:I.122, A:L.125, A:T.222, A:Y.226, A:I.300, A:I.300, A:I.304
Hydrogen bonds: A:G.80, A:D.81, A:S.83, A:D.219, A:T.222

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2:

5 residues within 4Å:

Chain A: D.81, G.221, T.222, T.223
Ligands: RB9.1

2 PLIP interactions:

2 interactions with chain A

Hydrogen bonds: A:T.223
Water bridges: A:L.224

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3:

6 residues within 4Å:

Chain A: V.272, P.274, Y.277, A.312, S.329, K.330

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:K.330, A:K.330
Water bridges: A:V.272

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

PG4.4:

7 residues within 4Å:

Chain A: G.37, S.78, Y.79, G.80, L.133, T.135
Ligands: RB9.1

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:S.78

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5:

7 residues within 4Å:

Chain A: D.15, L.224, Y.226, V.248, F.280, I.283, F.291

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:Y.226

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Kuhnert, M. et al., Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors. Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2011-12-07

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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Cartoon
Tube
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Licorice
Hyperball
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Surface
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Outline
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Background

Transparent

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