Structure of PDB 6nv9 Chain A Binding Site BS01

Receptor Information
>6nv9 Chain A (length=373) 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
PVEQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVH
DEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDL3M
InChIInChI=1S/C34H52N4O5S/c1-6-11-31(39)32(34(41)36-22-24(3)4)35-23-29-19-26-15-10-14-25(17-26)12-8-9-13-27-18-28(33(40)37-29)21-30(20-27)38(16-7-2)44(5,42)43/h10,14-15,17-18,20-21,24,29,31-32,35,39H,6-9,11-13,16,19,22-23H2,1-5H3,(H,36,41)(H,37,40)/t29-,31-,32-/m0/s1
InChIKeyBUVUUWHTEARFCT-GOBOWQCMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCC[C@H](O)[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 12.01O=C3c1cc(cc(c1)CCCCc2cc(ccc2)CC(CNC(C(CCC)O)C(=O)NCC(C)C)N3)N(CCC)S(C)(=O)=O
OpenEye OEToolkits 2.0.7CCCC(C(C(=O)NCC(C)C)NCC1Cc2cccc(c2)CCCCc3cc(cc(c3)N(CCC)S(=O)(=O)C)C(=O)N1)O
OpenEye OEToolkits 2.0.7CCC[C@@H]([C@@H](C(=O)NCC(C)C)NC[C@@H]1Cc2cccc(c2)CCCCc3cc(cc(c3)N(CCC)S(=O)(=O)C)C(=O)N1)O
CACTVS 3.385CCC[CH](O)[CH](NC[CH]1Cc2cccc(CCCCc3cc(cc(c3)C(=O)N1)N(CCC)[S](C)(=O)=O)c2)C(=O)NCC(C)C
FormulaC34 H52 N4 O5 S
Name(3S)-3-hydroxy-N-(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
ChEMBL
DrugBank
ZINC
PDB chain6nv9 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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PDB6nv9 Development of an Efficient Enzyme Production and Structure-Based Discovery Platform for BACE1 Inhibitors.
Resolution2.13 Å
Binding residue
(original residue number in PDB)
G11 Q12 L30 D32 G34 P70 Y71 T72 Q73 F108 Y198 D228 G230 T231 T232 N233 R235
Binding residue
(residue number reindexed from 1)
G14 Q15 L33 D35 G37 P73 Y74 T75 Q76 F111 Y191 D221 G223 T224 T225 N226 R228
Annotation score1
Binding affinityMOAD: Ki=7nM
PDBbind-CN: -logKd/Ki=8.19,Kd=6.4nM
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:6nv9, PDBe:6nv9, PDBj:6nv9
PDBsum6nv9
PubMed31549827
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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