Structure of PDB 4d89 Chain A Binding Site BS01

Receptor Information
>4d89 Chain A (length=375) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEING
QDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDG
FWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVE
DVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACH
VHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDBXD
InChIInChI=1S/C28H38F4N2O5S/c1-5-38-14-24(28(30,31)32)39-23-12-18(11-21(29)25(23)33)9-19-15-40(36,37)16-22(26(19)35)34-13-17-7-6-8-20(10-17)27(2,3)4/h6-8,10-12,19,22,24,26,34-35H,5,9,13-16,33H2,1-4H3/t19-,22+,24-,26+/m1/s1
InChIKeyUJZFSYZNJMWXJO-NJONLQHESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCOCC(C(F)(F)F)Oc1cc(cc(c1N)F)CC2CS(=O)(=O)CC(C2O)NCc3cccc(c3)C(C)(C)C
OpenEye OEToolkits 1.7.6CCOC[C@H](C(F)(F)F)Oc1cc(cc(c1N)F)C[C@@H]2CS(=O)(=O)C[C@@H]([C@H]2O)NCc3cccc(c3)C(C)(C)C
ACDLabs 12.01O=S2(=O)CC(C(O)C(NCc1cccc(c1)C(C)(C)C)C2)Cc3cc(F)c(N)c(OC(C(F)(F)F)COCC)c3
CACTVS 3.370CCOC[CH](Oc1cc(C[CH]2C[S](=O)(=O)C[CH](NCc3cccc(c3)C(C)(C)C)[CH]2O)cc(F)c1N)C(F)(F)F
CACTVS 3.370CCOC[C@@H](Oc1cc(C[C@@H]2C[S](=O)(=O)C[C@H](NCc3cccc(c3)C(C)(C)C)[C@H]2O)cc(F)c1N)C(F)(F)F
FormulaC28 H38 F4 N2 O5 S
Name(3S,4S,5R)-3-(4-amino-3-{[(2R)-3-ethoxy-1,1,1-trifluoropropan-2-yl]oxy}-5-fluorobenzyl)-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1,1-dioxide
ChEMBLCHEMBL2048051
DrugBank
ZINCZINC000084669160
PDB chain4d89 Chain A Residue 501 [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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PDB4d89 Discovery of cyclic sulfone hydroxyethylamines as potent and selective beta-site APP-cleaving enzyme 1 (BACE1) inhibitors: structure based design and in vivo reduction of amyloid beta-peptides
Resolution1.65 Å
Binding residue
(original residue number in PDB)		Q60 G61 L78 D80 G82 S83 P118 Y119 T120 Q121 F156 Y246 D276 G278 T279
Binding residue
(residue number reindexed from 1)		Q15 G16 L33 D35 G37 S38 P73 Y74 T75 Q76 F111 Y188 D218 G220 T221
Annotation score1
Binding affinityMOAD: ic50=0.002uM
PDBbind-CN: -logKd/Ki=8.70,IC50=0.002uM
Enzymatic activity
Catalytic site (original residue number in PDB) D80 S83 N85 A87 Y119 D276 T279
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 D218 T221
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:4d89, PDBe:4d89, PDBj:4d89
PDBsum4d89
PubMed22380629
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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