Structure of PDB 4bfd Chain A Binding Site BS01

Receptor Information
>4bfd Chain A (length=372) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPH
PFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTV
RANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTH
VPNLFSLQLCGSVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVE
INGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVASIKAASSTEKF
PDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLR
PVEDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHD
EFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID8T3
InChIInChI=1S/C19H18ClFN4O/c1-19(8-10-6-13(10)17(22)25-19)14-7-12(3-4-15(14)21)24-18(26)16-5-2-11(20)9-23-16/h2-5,7,9-10,13H,6,8H2,1H3,(H2,22,25)(H,24,26)/t10-,13-,19-/m0/s1
InChIKeyMELPDVINWCDKRF-JXBWDGJFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C[C@]1(C[C@@H]2C[C@@H]2C(=N1)N)c3cc(ccc3F)NC(=O)c4ccc(cn4)Cl
CACTVS 3.385C[C]1(C[CH]2C[CH]2C(=N1)N)c3cc(NC(=O)c4ccc(Cl)cn4)ccc3F
ACDLabs 12.01Clc1ccc(nc1)C(=O)Nc2cc(c(F)cc2)C4(N=C(N)C3CC3C4)C
CACTVS 3.385C[C@]1(C[C@@H]2C[C@@H]2C(=N1)N)c3cc(NC(=O)c4ccc(Cl)cn4)ccc3F
OpenEye OEToolkits 1.9.2CC1(CC2CC2C(=N1)N)c3cc(ccc3F)NC(=O)c4ccc(cn4)Cl
FormulaC19 H18 Cl F N4 O
NameN-[3-[(1S,3S,6S)-5-azanyl-3-methyl-4-azabicyclo[4.1.0]hept-4-en-3-yl]-4-fluoranyl-phenyl]-5-chloranyl-pyridine-2-carbox amide;
N-[3-[(1S,3S,6S)-5-amino-3-methyl-4-azabicyclo[4.1.0]hept-4-en-3-yl]-4-fluorophenyl]-5-chloropyridine-2-carboxamide
ChEMBLCHEMBL2403773
DrugBank
ZINCZINC000095920554
PDB chain4bfd Chain A Residue 1447 [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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PDB4bfd Bace1 Inhibitors: A Head Group Scan on a Series of Amides.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G72 Q73 G74 L91 D93 Y132 F169 D289 G291 T293
Binding residue
(residue number reindexed from 1)		G16 Q17 G18 L35 D37 Y76 F113 D221 G223 T225
Annotation score1
Binding affinityMOAD: ic50=0.096uM
PDBbind-CN: -logKd/Ki=7.02,IC50=96nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D37 S40 N42 A44 Y76 D221 T224
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:4bfd, PDBe:4bfd, PDBj:4bfd
PDBsum4bfd
PubMed23735744
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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