SMTL ID : 6qbg.1

Crystal structure of human cathepsin D in complex with macrocyclic inhibitor 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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 Chain B: V.8, N.40, V.41 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.40

2 x HVT: (3~{S},7~{S},8~{S})-8-(naphthalen-2-ylmethyl)-7-oxidanyl-3-propan-2-yl-1,4,9-triazacyclohenicosane-2,5,10-trione(Non-covalent)

HVT.2: 19 residues within 4Å: Chain A: D.33, G.35, S.36, I.76, H.77, Y.78, G.79, S.80 Chain B: T.19, F.20, I.28, I.36, Y.99, D.125, G.127, T.128, M.203, I.214 Ligands: DMS.3 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.76, A:Y.78, A:Y.78, B:F.20, B:I.28, B:I.36, B:I.214 Hydrogen bonds: A:D.33, A:G.35, A:H.77, A:G.79, A:S.80, B:T.128 pi-Stacking: B:F.25 HVT.6: 10 residues within 4Å: Chain B: I.18, T.19, L.150, I.151, Q.152, E.154, M.156, V.188, Q.190, L.195 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.18, B:L.150, B:I.151, B:V.188, B:V.188, B:V.188, B:Q.190, B:Q.190, B:L.195 Hydrogen bonds: B:E.154

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

DMS.3: 10 residues within 4Å: Chain A: A.13, Q.14, Y.15, V.31 Chain B: T.126, G.127, T.128, S.129, D.217 Ligands: HVT.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.15 Salt bridges: B:D.217 DMS.4: 3 residues within 4Å: Chain A: K.8, Y.16 Chain B: K.24 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.16 Hydrogen bonds: B:K.24

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

NAG.5: 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)

SO4.7: 5 residues within 4Å: Chain B: K.178, S.180, D.183, R.222, R.241 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.180, B:S.180 Salt bridges: B:K.178, B:R.222, B:R.241

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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