Structure of PDB 6nw3 Chain A Binding Site BS01

Receptor Information
>6nw3 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]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVE
INGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKF
PDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLR
PVDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDE
FRTAAVEGPFVTLDMEDCGY
Ligand information
Ligand IDL4J
InChIInChI=1S/C34H52N4O4S/c1-6-8-16-32(34(40)36-23-25(3)4)35-24-30-20-27-15-11-14-26(18-27)12-9-10-13-28-19-29(33(39)37-30)22-31(21-28)38(17-7-2)43(5,41)42/h11,14-15,18-19,21-22,25,30,32,35H,6-10,12-13,16-17,20,23-24H2,1-5H3,(H,36,40)(H,37,39)/t30-,32-/m0/s1
InChIKeyJRTACURQOKVHSE-CDZUIXILSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCCC[C@@H](C(=O)NCC(C)C)NC[C@@H]1Cc2cccc(c2)CCCCc3cc(cc(c3)N(CCC)S(=O)(=O)C)C(=O)N1
CACTVS 3.385CCCC[C@H](NC[C@@H]1Cc2cccc(CCCCc3cc(cc(c3)C(=O)N1)N(CCC)[S](C)(=O)=O)c2)C(=O)NCC(C)C
ACDLabs 12.01c32cccc(CC(NC(=O)c1cc(cc(c1)CCCC2)N(CCC)S(=O)(C)=O)CNC(C(=O)NCC(C)C)CCCC)c3
CACTVS 3.385CCCC[CH](NC[CH]1Cc2cccc(CCCCc3cc(cc(c3)C(=O)N1)N(CCC)[S](C)(=O)=O)c2)C(=O)NCC(C)C
OpenEye OEToolkits 2.0.7CCCCC(C(=O)NCC(C)C)NCC1Cc2cccc(c2)CCCCc3cc(cc(c3)N(CCC)S(=O)(=O)C)C(=O)N1
FormulaC34 H52 N4 O4 S
NameN-(2-methylpropyl)-N~2~-{[(4S)-17-[(methylsulfonyl)(propyl)amino]-2-oxo-3-azatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaen-4-yl]methyl}-L-norleucinamide
ChEMBLCHEMBL385374
DrugBank
ZINCZINC000014961984
PDB chain6nw3 Chain A Residue 401 [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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PDB6nw3 Development of an Efficient Enzyme Production and Structure-Based Discovery Platform for BACE1 Inhibitors.
Resolution2.352 Å
Binding residue
(original residue number in PDB)		L30 D32 G34 P70 Y71 T72 Q73 F108 Y198 D228 G230 T231 T232 N233 R235 T329
Binding residue
(residue number reindexed from 1)		L33 D35 G37 P73 Y74 T75 Q76 F111 Y191 D221 G223 T224 T225 N226 R228 T315
Annotation score1
Binding affinityMOAD: Ki=21nM
PDBbind-CN: -logKd/Ki=7.66,Kd=22.1nM
BindingDB: IC50=4nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 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:6nw3, PDBe:6nw3, PDBj:6nw3
PDBsum6nw3
PubMed31549827
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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