Structure of PDB 4rcf Chain A Binding Site BS01

Receptor Information
>4rcf Chain A (length=370) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFR
TAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID3LO
InChIInChI=1S/C25H19F2N3O3/c26-20-12-16(14-5-8-31-9-6-14)11-19-22(20)33-21-4-3-15(17-2-1-7-29-23(17)27)10-18(21)25(19)13-32-24(28)30-25/h1-5,7,10-12H,6,8-9,13H2,(H2,28,30)/t25-/m0/s1
InChIKeyUBJVRJGPVXTXQB-VWLOTQADSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=N[C@@]2(CO1)c3cc(ccc3Oc4c(F)cc(cc24)C5=CCOCC5)c6cccnc6F
ACDLabs 12.01Fc1ncccc1c6cc5c(Oc3c(F)cc(C2=CCOCC2)cc3C54N=C(OC4)N)cc6
OpenEye OEToolkits 1.7.6c1cc(c(nc1)F)c2ccc3c(c2)[C@@]4(COC(=N4)N)c5cc(cc(c5O3)F)C6=CCOCC6
OpenEye OEToolkits 1.7.6c1cc(c(nc1)F)c2ccc3c(c2)C4(COC(=N4)N)c5cc(cc(c5O3)F)C6=CCOCC6
CACTVS 3.385NC1=N[C]2(CO1)c3cc(ccc3Oc4c(F)cc(cc24)C5=CCOCC5)c6cccnc6F
FormulaC25 H19 F2 N3 O3
Name(4S)-2'-(3,6-dihydro-2H-pyran-4-yl)-4'-fluoro-7'-(2-fluoropyridin-3-yl)spiro[1,3-oxazole-4,9'-xanthen]-2-amine
ChEMBLCHEMBL3354718
DrugBank
ZINCZINC000117733754
PDB chain4rcf Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4rcf Lead Optimization and Modulation of hERG Activity in a Series of Aminooxazoline Xanthene beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE1) Inhibitors.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		G11 Q12 G13 L30 D32 Y71 W76 F108 R128 D228 G230
Binding residue
(residue number reindexed from 1)		G13 Q14 G15 L32 D34 Y73 W78 F110 R130 D220 G222
Annotation score1
Binding affinityMOAD: ic50=4nM
PDBbind-CN: -logKd/Ki=8.40,IC50=4nM
BindingDB: IC50=4.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D34 S37 N39 A41 Y73 D220 T223
Enzyme Commision number 3.4.23.46: memapsin 2.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4rcf, PDBe:4rcf, PDBj:4rcf
PDBsum4rcf
PubMed25389560
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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