Structure of PDB 5ux4 Chain A Binding Site BS01

Receptor Information
>5ux4 Chain A (length=337) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPVSELLKNYLDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLD
IACWVHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCKGGI
KVEKQIFGEATKQPGVVFIAAKFDGILGMGYPFISVNNVLPVFDNLMKQK
LVEKNIFSFYLNRDPTGQPGGELMLGGTDSRYYHGELSYLNVTRKAYWQV
HMDQLEVGSELTLCKGGCEAIVDTGTSLLVGPVDEVKELQKAIGAVPLIQ
GEYMIPCEKVSSLPIITFKLGGQNYELHPEKYILKVSKTICLSGFMGMDI
PPPSGPLWILGDVFIGCYYTVFDREYNRVGFAKAATL
Ligand information
Ligand ID3UT
InChIInChI=1S/C24H18F2N4O3/c25-21-15(4-1-7-28-21)13-5-6-19-16(9-13)24(12-32-23(27)30-24)17-10-18(14-3-2-8-31-11-14)29-22(26)20(17)33-19/h1,3-7,9-10H,2,8,11-12H2,(H2,27,30)/t24-/m0/s1
InChIKeyJAZOCUNZCUBRJX-DEOSSOPVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc(c(nc1)F)c2ccc3c(c2)[C@@]4(COC(=N4)N)c5cc(nc(c5O3)F)C6=CCCOC6
CACTVS 3.385NC1=N[C]2(CO1)c3cc(ccc3Oc4c(F)nc(cc24)C5=CCCOC5)c6cccnc6F
CACTVS 3.385NC1=N[C@@]2(CO1)c3cc(ccc3Oc4c(F)nc(cc24)C5=CCCOC5)c6cccnc6F
OpenEye OEToolkits 1.9.2c1cc(c(nc1)F)c2ccc3c(c2)C4(COC(=N4)N)c5cc(nc(c5O3)F)C6=CCCOC6
ACDLabs 12.01Fc1ncccc1c6cc5c(Oc3c(F)nc(C2=CCCOC2)cc3C54N=C(OC4)N)cc6
FormulaC24 H18 F2 N4 O3
Name(5S)-3-(5,6-dihydro-2H-pyran-3-yl)-1-fluoro-7-(2-fluoropyridin-3-yl)spiro[chromeno[2,3-c]pyridine-5,4'-[1,3]oxazol]-2'-amine
ChEMBLCHEMBL4564735
DrugBank
ZINCZINC000072317156
PDB chain5ux4 Chain A Residue 404 [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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PDB5ux4 Development of 2-aminooxazoline 3-azaxanthene beta-amyloid cleaving enzyme (BACE) inhibitors with improved selectivity against Cathepsin D.
Resolution2.805 Å
Binding residue
(original residue number in PDB)		D33 I76 Y78 I129 D226 G228
Binding residue
(residue number reindexed from 1)		D33 I76 Y78 I126 D223 G225
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.05,IC50=0.09uM
Enzymatic activity
Enzyme Commision number 3.4.23.5: cathepsin D.
Gene Ontology
Molecular Function
GO:0004175 endopeptidase activity
GO:0004190 aspartic-type endopeptidase activity
GO:0008233 peptidase activity
GO:0016787 hydrolase activity
GO:0042277 peptide binding
GO:0070001 aspartic-type peptidase activity
Biological Process
GO:0000045 autophagosome assembly
GO:0006508 proteolysis
GO:0030163 protein catabolic process
GO:0031667 response to nutrient levels
GO:0038020 insulin receptor recycling
GO:0042159 lipoprotein catabolic process
GO:0043065 positive regulation of apoptotic process
GO:0060441 epithelial tube branching involved in lung morphogenesis
GO:0070201 regulation of establishment of protein localization
GO:0099003 vesicle-mediated transport in synapse
GO:0099532 synaptic vesicle endosomal processing
GO:1901143 insulin catabolic process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0010008 endosome membrane
GO:0031904 endosome lumen
GO:0042470 melanosome
GO:0045121 membrane raft
GO:0098830 presynaptic endosome
GO:0098982 GABA-ergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ux4, PDBe:5ux4, PDBj:5ux4
PDBsum5ux4
PubMed30108829
UniProtP24268|CATD_RAT Cathepsin D (Gene Name=Ctsd)

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