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BioLiP

Structure of PDB 4obz Chain A Binding Site BS01

Receptor Information
>4obz Chain A (length=97) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDI
ACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQS
Ligand information
Ligand ID2S4
InChIInChI=1S/C19H23N3O3/c1-13-4-6-14(7-5-13)12-21-19(20)22-18(23)11-15-8-9-16(24-2)17(10-15)25-3/h4-10H,11-12H2,1-3H3,(H3,20,21,22,23)
InChIKeyLDSKOSCPBKZJCO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NC(=[N@H])NCc1ccc(cc1)C)Cc2cc(OC)c(OC)cc2
OpenEye OEToolkits 1.7.6[H]/N=C(/NCc1ccc(cc1)C)\NC(=O)Cc2ccc(c(c2)OC)OC
CACTVS 3.385COc1ccc(CC(=O)NC(=N)NCc2ccc(C)cc2)cc1OC
OpenEye OEToolkits 1.7.6Cc1ccc(cc1)CNC(=N)NC(=O)Cc2ccc(c(c2)OC)OC
FormulaC19 H23 N3 O3
Name2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide
ChEMBLCHEMBL3321915
DrugBank
ZINCZINC000098208254
PDB chain4obz Chain B Residue 401 [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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PDB4obz Structure-based optimization of non-peptidic Cathepsin D inhibitors.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D33 Y78
Binding residue
(residue number reindexed from 1)		D32 Y77
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.72,IC50=1.9uM
BindingDB: IC50=1900nM
Enzymatic activity
Catalytic site (original residue number in PDB) D33 S36 N38 W40 Y78
Catalytic site (residue number reindexed from 1) D32 S35 N37 W39 Y77
Enzyme Commision number 3.4.23.5: cathepsin D.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:4obz, PDBe:4obz, PDBj:4obz
PDBsum4obz
PubMed25086681
UniProtP07339|CATD_HUMAN Cathepsin D (Gene Name=CTSD)

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