Structure of PDB 6qbg Chain A Binding Site BS01

Receptor Information

>6qbg Chain A (length=98) Species: 9606 (Homo sapiens)

GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLD
IACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQS

Ligand information

• Ligand ID: HVT
• InChI: InChI=1S/C32H47N3O4/c1-23(2)31-32(39)33-19-13-9-7-5-3-4-6-8-10-16-29(37)34-27(28(36)22-30(38)35-31)21-24-17-18-25-14-11-12-15-26(25)20-24/h11-12,14-15,17-18,20,23,27-28,31,36H,3-10,13,16,19,21-22H2,1-2H3,(H,33,39)(H,34,37)(H,35,38)/t27-,28-,31-/m0/s1
• InChIKey: YVZCVARIDAMNNV-QYDYLWNGSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(C)C1C(=O)NCCCCCCCCCCCC(=O)NC(C(CC(=O)N1)O)Cc2ccc3ccccc3c2
  OpenEye OEToolkits 2.0.6: CC(C)[C@H]1C(=O)NCCCCCCCCCCCC(=O)N[C@H]([C@H](CC(=O)N1)O)Cc2ccc3ccccc3c2
  CACTVS 3.385: CC(C)[CH]1NC(=O)C[CH](O)[CH](Cc2ccc3ccccc3c2)NC(=O)CCCCCCCCCCCNC1=O
  CACTVS 3.385: CC(C)[C@@H]1NC(=O)C[C@H](O)[C@H](Cc2ccc3ccccc3c2)NC(=O)CCCCCCCCCCCNC1=O
• Formula: C32 H47 N3 O4
• Name: (3~{S},7~{S},8~{S})-8-(naphthalen-2-ylmethyl)-7-oxidanyl-3-propan-2-yl-1,4,9-triazacyclohenicosane-2,5,10-trione
• ChEMBL: CHEMBL4576166
• PDB chain: 6qbg Chain A Residue 103

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qbg Biomimetic Macrocyclic Inhibitors of Human Cathepsin D: Structure-Activity Relationship and Binding Mode Analysis.
• Resolution: 1.8 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=0.6nM
  BindingDB: IC50=0.600000nM

Enzymatic activity

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