Structure of PDB 6qbg Chain B Binding Site BS02

Receptor Information
>6qbg 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 IDHVT
InChIInChI=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
InChIKeyYVZCVARIDAMNNV-QYDYLWNGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)C1C(=O)NCCCCCCCCCCCC(=O)NC(C(CC(=O)N1)O)Cc2ccc3ccccc3c2
OpenEye OEToolkits 2.0.6CC(C)[C@H]1C(=O)NCCCCCCCCCCCC(=O)N[C@H]([C@H](CC(=O)N1)O)Cc2ccc3ccccc3c2
CACTVS 3.385CC(C)[CH]1NC(=O)C[CH](O)[CH](Cc2ccc3ccccc3c2)NC(=O)CCCCCCCCCCCNC1=O
CACTVS 3.385CC(C)[C@@H]1NC(=O)C[C@H](O)[C@H](Cc2ccc3ccccc3c2)NC(=O)CCCCCCCCCCCNC1=O
FormulaC32 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
ChEMBLCHEMBL4576166
DrugBank
ZINC
PDB chain6qbg Chain B Residue 402 [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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PDB6qbg Biomimetic Macrocyclic Inhibitors of Human Cathepsin D: Structure-Activity Relationship and Binding Mode Analysis.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		I257 E260 V294 Q296
Binding residue
(residue number reindexed from 1)		I151 E154 V188 Q190
Annotation score1
Binding affinityMOAD: 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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:6qbg, PDBe:6qbg, PDBj:6qbg
PDBsum6qbg
PubMed32003991
UniProtP07339|CATD_HUMAN Cathepsin D (Gene Name=CTSD)

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