SMTL ID : 4od9.1

Structure of Cathepsin D with inhibitor N-(3,4-dimethoxybenzyl)-Nalpha-{N-[(3,4-dimethoxyphenyl)acetyl]carbamimidoyl}-D-phenylalaninamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 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: 6 residues within 4Å: Chain A: N.75, T.77, L.92 Chain B: N.40, N.41, V.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.40 NAG-NAG.5: 7 residues within 4Å: Chain C: N.75, T.77, L.92 Chain D: V.9, N.40, N.41, V.42 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.40

2 x 2RZ: N-(3,4-dimethoxybenzyl)-Nalpha-{N-[(3,4-dimethoxyphenyl)acetyl]carbamimidoyl}-D-phenylalaninamide(Non-covalent)

2RZ.2: 20 residues within 4Å: Chain A: A.18, D.38, G.40, Y.83, G.84, S.85 Chain B: T.20, F.21, F.26, I.29, Y.100, I.124, D.126, G.128, T.129, M.204, D.205, I.206, I.215 Ligands: ACT.4 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.21, B:I.29, B:Y.100, B:I.124, B:I.206, B:I.206, B:I.215, A:Y.83 Hydrogen bonds: B:T.129, B:T.129, A:G.84, A:S.85 Salt bridges: B:D.126, A:D.38 pi-Stacking: B:F.26 Water bridges: A:Q.19, A:Q.19 2RZ.7: 20 residues within 4Å: Chain C: A.18, D.38, G.40, Y.83, G.84, S.85 Chain D: T.20, F.21, F.26, I.29, Y.100, I.124, D.126, G.128, T.129, M.204, D.205, I.206, I.215 Ligands: ACT.6 16 PLIP interactions: 11 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.21, D:I.29, D:Y.100, D:I.124, D:I.206, D:I.215, C:Y.83 Hydrogen bonds: D:T.129, D:T.129, D:T.129, C:G.40, C:G.84, C:S.85 Salt bridges: D:D.126, C:D.38 pi-Stacking: D:F.26

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

NAG.3: 1 residues within 4Å: Chain B: N.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.94

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain B: G.128, T.129, S.130 Ligands: 2RZ.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.130 Water bridges: B:S.130, B:L.131 ACT.6: 4 residues within 4Å: Chain D: G.128, T.129, S.130 Ligands: 2RZ.7 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.130 Water bridges: D:L.131

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
A

C
C

B
B

D
D

Cathepsin D light chain

Cathepsin D heavy chain

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