Structure of PDB 6qbh Chain A Binding Site BS01

Receptor Information

>6qbh Chain A (length=97) Species: 9606 (Homo sapiens)

GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLD
IACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQ

Ligand information

• Ligand ID: S43
• InChI: InChI=1S/C28H45N3O5/c1-21(2)26-27(34)29-17-13-8-6-4-3-5-7-9-14-18-36-28(35)30-23(24(32)20-25(33)31-26)19-22-15-11-10-12-16-22/h10-12,15-16,21,23-24,26,32H,3-9,13-14,17-20H2,1-2H3,(H,29,34)(H,30,35)(H,31,33)/t23-,24-,26-/m0/s1
• InChIKey: ISMDILRWKSYCOD-GNKBHMEESA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(C)[C@H]1C(=O)NCCCCCCCCCCCOC(=O)N[C@H]([C@H](CC(=O)N1)O)Cc2ccccc2
  CACTVS 3.385: CC(C)[C@@H]1NC(=O)C[C@H](O)[C@H](Cc2ccccc2)NC(=O)OCCCCCCCCCCCNC1=O
  CACTVS 3.385: CC(C)[CH]1NC(=O)C[CH](O)[CH](Cc2ccccc2)NC(=O)OCCCCCCCCCCCNC1=O
  OpenEye OEToolkits 2.0.6: CC(C)C1C(=O)NCCCCCCCCCCCOC(=O)NC(C(CC(=O)N1)O)Cc2ccccc2
• Formula: C28 H45 N3 O5
• Name: (4~{S},5~{S},9~{S})-5-oxidanyl-4-(phenylmethyl)-9-propan-2-yl-1-oxa-3,8,11-triazacyclodocosane-2,7,10-trione
• ChEMBL: CHEMBL4514021
• PDB chain: 6qbh Chain A Residue 103

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qbh Biomimetic Macrocyclic Inhibitors of Human Cathepsin D: Structure-Activity Relationship and Binding Mode Analysis.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): D33 G35 H77 Y78 G79 S80
• Binding residue (residue number reindexed from 1): D33 G35 H77 Y78 G79 S80
• Annotation score: 1
• Binding affinity: MOAD: ic50=2.5nM
  BindingDB: IC50=2.5nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D33 S36 N38 W40 Y78
• Catalytic site (residue number reindexed from 1): D33 S36 N38 W40 Y78
• Enzyme Commision number: 3.4.23.5: cathepsin D.

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:6qbh, PDBe:6qbh, PDBj:6qbh
• PDBsum: 6qbh
• PubMed: 32003991
• UniProt: P07339|CATD_HUMAN Cathepsin D (Gene Name=CTSD)