SMTL ID : 6qbh.1

Crystal structure of human cathepsin D in complex with macrocyclic inhibitor 33

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-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: 4 residues within 4Å: Chain A: N.70, T.72 Chain B: V.8, N.40 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.40

1 x S43: (4~{S},5~{S},9~{S})-5-oxidanyl-4-(phenylmethyl)-9-propan-2-yl-1-oxa-3,8,11-triazacyclodocosane-2,7,10-trione(Non-covalent)

S43.2: 17 residues within 4Å: Chain A: D.33, G.35, S.36, H.77, Y.78, G.79, S.80 Chain B: F.20, F.25, I.28, I.36, Y.99, D.125, G.127, T.128, M.203, I.214 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.20, B:F.25, B:I.28, B:I.36, B:I.214, A:Y.78 Hydrogen bonds: B:G.127, A:G.35, A:G.35, A:G.35, A:H.77, A:G.79, A:S.80 pi-Stacking: A:Y.78

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

NAG.3: 1 residues within 4Å: Chain B: N.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.93

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain B: K.178, S.180, R.222, R.241 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.180 Salt bridges: B:K.178, B:R.222, B:R.241

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

DMS.5: 2 residues within 4Å: Chain B: Y.91, R.233 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.233, B:R.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Houstecka, R. et al., Biomimetic Macrocyclic Inhibitors of Human Cathepsin D: Structure-Activity Relationship and Binding Mode Analysis. J.Med.Chem. (2020)

Release Date

2020-01-29

Peptides

Cathepsin D: A
Cathepsin D: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cathepsin D

Cathepsin D

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