SMTL ID : 6qcb.1

Crystal structure of human cathepsin D in complex with macrocyclic inhibitor 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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: K.69, N.70 Chain B: V.8, N.40 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.40

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

NAG-NAG-BMA.2: 1 residues within 4Å: Chain B: N.93 No protein-ligand interaction detected (PLIP)

1 x PO3: PHOSPHITE ION(Non-covalent)

PO3.3: 3 residues within 4Å: Chain A: K.8, Y.16 Chain B: K.24 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.16 Water bridges: A:Y.16 Salt bridges: A:K.8, B:K.24

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

HWE.4: 18 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 Ligands: DMS.5 13 PLIP interactions: 6 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.78, B:F.20, B:F.25, B:I.28, B:I.36, B:I.214 Hydrogen bonds: A:G.35, A:H.77, A:G.79, A:S.80, B:D.125, B:T.128 pi-Stacking: A:Y.78

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

DMS.5: 11 residues within 4Å: Chain A: A.13, Q.14, Y.15, V.31 Chain B: F.25, T.126, G.127, T.128, S.129, D.217 Ligands: HWE.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:D.217 Hydrogen bonds: A:Y.15

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

SO4.6: 2 residues within 4Å: Chain B: R.35, R.96 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.35, B:R.96 SO4.7: 4 residues within 4Å: Chain B: K.178, S.180, R.222, R.241 3 PLIP interactions: 3 interactions with chain B 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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