Structure of PDB 3msl Chain A Binding Site BS01

Receptor Information
>3msl Chain A (length=377) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGAASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSA
CHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDEV5
InChIInChI=1S/C19H27ClN4O/c1-2-15(11-18(25)22-12-13-6-4-3-5-7-13)24-17-9-8-14(20)10-16(17)23-19(24)21/h8-10,13,15H,2-7,11-12H2,1H3,(H2,21,23)(H,22,25)/t15-/m0/s1
InChIKeyUKACQFCXAAAWAE-HNNXBMFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCC(CC(=O)NCC1CCCCC1)n2c3ccc(cc3nc2N)Cl
ACDLabs 12.01O=C(NCC1CCCCC1)CC(n2c3ccc(Cl)cc3nc2N)CC
CACTVS 3.370CC[CH](CC(=O)NCC1CCCCC1)n2c(N)nc3cc(Cl)ccc23
OpenEye OEToolkits 1.7.0CC[C@@H](CC(=O)NCC1CCCCC1)n2c3ccc(cc3nc2N)Cl
CACTVS 3.370CC[C@@H](CC(=O)NCC1CCCCC1)n2c(N)nc3cc(Cl)ccc23
FormulaC19 H27 Cl N4 O
Name(3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-(cyclohexylmethyl)pentanamide
ChEMBLCHEMBL1222240
DrugBank
ZINCZINC000058583410
PDB chain3msl Chain A Residue 395 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3msl Fragment-based discovery and optimization of BACE1 inhibitors.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D32 Y71 W76 F108 D228 G230
Binding residue
(residue number reindexed from 1)		D34 Y73 W78 F110 D220 G222
Annotation score1
Binding affinityMOAD: ic50=7uM
PDBbind-CN: -logKd/Ki=5.15,IC50=7uM
BindingDB: IC50=7000nM
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:3msl, PDBe:3msl, PDBj:3msl
PDBsum3msl
PubMed20656487
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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