Structure of PDB 3qi1 Chain A Binding Site BS01

Receptor Information
>3qi1 Chain A (length=382) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGAWAGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAGVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVII
VRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASS
TEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQ
QYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIG
FAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDC6A
InChIInChI=1S/C29H38F2N2O3/c1-17(34)33-25(12-19-9-21(30)13-22(31)10-19)26(35)16-32-24-14-28(20-6-7-20)36-27-8-5-18(11-23(24)27)15-29(2,3)4/h5,8-11,13,20,24-26,28,32,35H,6-7,12,14-16H2,1-4H3,(H,33,34)/t24-,25-,26+,28+/m0/s1
InChIKeyIBLLHMQPQAMFLM-WDTRASESSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(=O)N[C@@H](Cc1cc(F)cc(F)c1)[C@H](O)CN[C@H]2C[C@@H](Oc3ccc(CC(C)(C)C)cc23)C4CC4
OpenEye OEToolkits 1.7.0CC(=O)N[C@@H](Cc1cc(cc(c1)F)F)[C@@H](CN[C@H]2C[C@@H](Oc3c2cc(cc3)CC(C)(C)C)C4CC4)O
OpenEye OEToolkits 1.7.0CC(=O)NC(Cc1cc(cc(c1)F)F)C(CNC2CC(Oc3c2cc(cc3)CC(C)(C)C)C4CC4)O
CACTVS 3.370CC(=O)N[CH](Cc1cc(F)cc(F)c1)[CH](O)CN[CH]2C[CH](Oc3ccc(CC(C)(C)C)cc23)C4CC4
ACDLabs 12.01Fc1cc(cc(F)c1)CC(NC(=O)C)C(O)CNC2c4c(OC(C2)C3CC3)ccc(c4)CC(C)(C)C
FormulaC29 H38 F2 N2 O3
NameN-[(2S,3R)-4-{[(2R,4S)-2-cyclopropyl-6-(2,2-dimethylpropyl)-3,4-dihydro-2H-chromen-4-yl]amino}-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]acetamide
ChEMBL
DrugBank
ZINCZINC000098208726
PDB chain3qi1 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qi1 Design and synthesis of hydroxyethylamine (HEA) BACE-1 inhibitors: prime side chromane-containing inhibitors.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D38 G40 P76 Y77 T78 F114 Y204 K230 D234 G236
Binding residue
(residue number reindexed from 1)		D36 G38 P74 Y75 T76 F112 Y195 K221 D225 G227
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.66,IC50=22nM
Enzymatic activity
Catalytic site (original residue number in PDB) D38 S41 N43 A45 Y77 D234 T237
Catalytic site (residue number reindexed from 1) D36 S39 N41 A43 Y75 D225 T228
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:3qi1, PDBe:3qi1, PDBj:3qi1
PDBsum3qi1
PubMed23856050
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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