Structure of PDB 5ux4 Chain B Binding Site BS01

Receptor Information
>5ux4 Chain B (length=340) 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
GEYMIPCEKVSSLPIITFKLGGQNYELHPEKYILKVSQAGKTICLSGFMG
MDIPPPSGPLWILGDVFIGCYYTVFDREYNRVGFAKAATL
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 B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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 G35 S36 I76 Y78 I129 D226 G228
Binding residue
(residue number reindexed from 1)		D33 G35 S36 I76 Y78 I126 D223 G225
Annotation score1
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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