Structure of PDB 4oc6 Chain B Binding Site BS01

Receptor Information
>4oc6 Chain B (length=243) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GGVKVERQVFGEATKQPGITFIAAKFDGILGMAYPRISVNNVLPVFDNLM
QQKLVDQNIFSFYLSRDPDAQPGGELMLGGTDSKYYKGSLSYLNVTRKAY
WQVHLDQVEVASGLTLCKEGCEAIVDTGTSLMVGPVDEVRELQKAIGAVP
LIQGEYMIPCEKVSTLPAITLKLGGKGYKLSPEDYTLKVSQAGKTLCLSG
FMGMDIPPPSGPLWILGDVFIGRYYTVFDRDNNRVGFAEAARL
Ligand information
Ligand ID2S1
InChIInChI=1S/C44H40BrCl2N3O8/c1-56-39-24-34(35(45)25-40(39)57-2)42(53)48-37(22-27-9-8-12-31(21-27)58-30-10-4-3-5-11-30)38(51)26-49(19-17-28-15-16-29(46)23-36(28)47)41(52)18-20-50-43(54)32-13-6-7-14-33(32)44(50)55/h3-16,21,23-25,37-38,51H,17-20,22,26H2,1-2H3,(H,48,53)/t37-,38-/m0/s1
InChIKeyDQHKQRXAVNDAFY-UWXQCODUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6COc1cc(c(cc1OC)Br)C(=O)N[C@@H](Cc2cccc(c2)Oc3ccccc3)[C@H](CN(CCc4ccc(cc4Cl)Cl)C(=O)CCN5C(=O)c6ccccc6C5=O)O
CACTVS 3.385COc1cc(Br)c(cc1OC)C(=O)N[C@@H](Cc2cccc(Oc3ccccc3)c2)[C@@H](O)CN(CCc4ccc(Cl)cc4Cl)C(=O)CCN5C(=O)c6ccccc6C5=O
OpenEye OEToolkits 1.7.6COc1cc(c(cc1OC)Br)C(=O)NC(Cc2cccc(c2)Oc3ccccc3)C(CN(CCc4ccc(cc4Cl)Cl)C(=O)CCN5C(=O)c6ccccc6C5=O)O
CACTVS 3.385COc1cc(Br)c(cc1OC)C(=O)N[CH](Cc2cccc(Oc3ccccc3)c2)[CH](O)CN(CCc4ccc(Cl)cc4Cl)C(=O)CCN5C(=O)c6ccccc6C5=O
ACDLabs 12.01Brc1cc(OC)c(OC)cc1C(=O)NC(Cc3cccc(Oc2ccccc2)c3)C(O)CN(C(=O)CCN5C(=O)c4ccccc4C5=O)CCc6ccc(Cl)cc6Cl
FormulaC44 H40 Br Cl2 N3 O8
Name2-bromo-N-[(2S,3S)-4-{[2-(2,4-dichlorophenyl)ethyl][3-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propanoyl]amino}-3-hydroxy-1-(3-phenoxyphenyl)butan-2-yl]-4,5-dimethoxybenzamide
ChEMBLCHEMBL81927
DrugBank
ZINCZINC000150340387
PDB chain4oc6 Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4oc6 Structure-based optimization of non-peptidic Cathepsin D inhibitors.
Resolution2.64 Å
Binding residue
(original residue number in PDB)		T125 F131 I134 I142 Y205 D231 G233 T234 S235 I311 S315
Binding residue
(residue number reindexed from 1)		T20 F26 I29 I37 Y100 D126 G128 T129 S130 I206 S210
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.07,IC50=85nM
BindingDB: IC50=85nM,Ki=0.700000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D231 T234
Catalytic site (residue number reindexed from 1) D126 T129
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:4oc6, PDBe:4oc6, PDBj:4oc6
PDBsum4oc6
PubMed25086681
UniProtP07339|CATD_HUMAN Cathepsin D (Gene Name=CTSD)

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