Structure of PDB 6qbh Chain B Binding Site BS01

Receptor Information
>6qbh Chain B (length=241) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLMQ
QKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAYW
QVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVPL
IQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSGF
MGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAAR
Ligand information
Ligand IDS43
InChIInChI=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
InChIKeyISMDILRWKSYCOD-GNKBHMEESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)[C@H]1C(=O)NCCCCCCCCCCCOC(=O)N[C@H]([C@H](CC(=O)N1)O)Cc2ccccc2
CACTVS 3.385CC(C)[C@@H]1NC(=O)C[C@H](O)[C@H](Cc2ccccc2)NC(=O)OCCCCCCCCCCCNC1=O
CACTVS 3.385CC(C)[CH]1NC(=O)C[CH](O)[CH](Cc2ccccc2)NC(=O)OCCCCCCCCCCCNC1=O
OpenEye OEToolkits 2.0.6CC(C)C1C(=O)NCCCCCCCCCCCOC(=O)NC(C(CC(=O)N1)O)Cc2ccccc2
FormulaC28 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
ChEMBLCHEMBL4514021
DrugBank
ZINC
PDB chain6qbh Chain A Residue 103 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6qbh Biomimetic Macrocyclic Inhibitors of Human Cathepsin D: Structure-Activity Relationship and Binding Mode Analysis.
Resolution1.85 Å
Binding residue
(original residue number in PDB)
F126 F131 I134 Y205 D231 G233 M309 I320
Binding residue
(residue number reindexed from 1)
F20 F25 I28 Y99 D125 G127 M203 I214
Annotation score1
Binding affinityBindingDB: IC50=2.5nM
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

View graph for
Molecular Function

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Biological Process
External links
PDB RCSB:6qbh, PDBe:6qbh, PDBj:6qbh
PDBsum6qbh
PubMed32003991
UniProtP07339|CATD_HUMAN Cathepsin D (Gene Name=CTSD)

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