SMTL ID : 4obz.1

Structure of Cathepsin D with inhibitor 2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-2-2-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.75, T.77 Chain B: V.9, N.40, N.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.40

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 3 residues within 4Å: Chain C: N.75, T.77 Chain D: V.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.77, C:T.77

1 x 2S4: 2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide(Non-covalent)

2S4.3: 16 residues within 4Å: Chain C: Q.19, D.38, G.40, Y.83, S.85 Chain D: T.20, F.21, F.26, I.29, Y.100, I.124, D.126, G.128, T.129, I.206, I.215 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:Y.83, D:I.29, D:Y.100, D:Y.100, D:I.124, D:I.206, D:I.206, D:I.215 Hydrogen bonds: C:S.85, D:T.129 Salt bridges: C:D.38, D:D.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gradler, U. et al., Structure-based optimization of non-peptidic Cathepsin D inhibitors. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-08-13

Peptides

Cathepsin D light chain: AC
Cathepsin D heavy chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

B
D

D
B

Cathepsin D light chain

Cathepsin D heavy chain

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