SMTL ID : 4oc6.1

Structure of Cathepsin D with inhibitor 2-bromo-N-[(2S,3S)-4-{[2-(2,4-dichlorophenyl)ethyl][3-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propanoyl]amino}-3-hydroxy-1-(3-phenoxyphenyl)butan-2-yl]-4,5-dimethoxybenzamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 6 residues within 4Å: Chain A: N.75, T.77 Chain B: V.9, N.40, N.41, V.42 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.40 NAG-NAG-BMA-MAN.5: 6 residues within 4Å: Chain C: N.75, T.77 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 NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain B: N.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.94 NAG.6: 1 residues within 4Å: Chain D: N.94 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.94

2 x 2S1: 2-bromo-N-[(2S,3S)-4-{[2-(2,4-dichlorophenyl)ethyl][3-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propanoyl]amino}-3-hydroxy-1-(3-phenoxyphenyl)butan-2-yl]-4,5-dimethoxybenzamide(Non-covalent)

2S1.3: 25 residues within 4Å: Chain A: A.18, D.38, G.40, S.41, H.82, Y.83, G.84, S.85 Chain B: T.20, A.23, A.24, F.26, I.29, I.37, Y.100, I.124, D.126, G.128, T.129, S.130, E.155, I.206, S.210, I.215 Ligands: GOL.4 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.20, B:A.23, B:F.26, B:F.26, B:I.29, B:I.37, B:Y.100, B:I.124, B:T.129, B:I.206, B:I.215, A:Y.83 Hydrogen bonds: B:G.128, B:S.130, A:D.38, A:G.84, A:S.85 pi-Stacking: A:Y.83 2S1.7: 25 residues within 4Å: Chain C: A.18, D.38, G.40, S.41, H.82, Y.83, G.84, S.85 Chain D: T.20, A.23, A.24, F.26, I.29, I.37, Y.100, I.124, D.126, G.128, T.129, S.130, E.155, I.206, S.210, I.215 Ligands: GOL.8 20 PLIP interactions: 15 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:T.20, D:A.23, D:F.26, D:F.26, D:I.29, D:I.37, D:Y.100, D:I.124, D:T.129, D:I.206, D:I.215, C:Y.83 Hydrogen bonds: D:Y.100, D:G.128, D:T.129, D:S.130, C:D.38, C:G.84, C:S.85 pi-Stacking: C:Y.83

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.84 Chain B: Q.153, M.202, M.204 Ligands: 2S1.3 No protein-ligand interaction detected (PLIP) GOL.8: 5 residues within 4Å: Chain C: G.84 Chain D: Q.153, M.202, M.204 Ligands: 2S1.7 No protein-ligand interaction detected (PLIP)

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
A

B
B

D
B

Cathepsin D light chain

Cathepsin D heavy chain

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