Structure of PDB 4obz Chain B Binding Site BS01

Receptor Information
>4obz Chain B (length=240) 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
MGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAA
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
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PDB4obz Structure-based optimization of non-peptidic Cathepsin D inhibitors.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		F131 I134 Y205 I229 D231
Binding residue
(residue number reindexed from 1)		F25 I28 Y99 I123 D125
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.72,IC50=1.9uM
BindingDB: IC50=1900nM
Enzymatic activity
Catalytic site (original residue number in PDB) D231 T234
Catalytic site (residue number reindexed from 1) D125 T128
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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