Structure of PDB 3u6a Chain A Binding Site BS01

Receptor Information
>3u6a Chain A (length=374) 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
PVESQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHV
HDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID18P
InChIInChI=1S/C18H18ClN5O2/c1-18(17(26)24(2)10-15(20)23-18)11-4-3-5-13(8-11)22-16(25)14-7-6-12(19)9-21-14/h3-9H,10H2,1-2H3,(H2,20,23)(H,22,25)/t18-/m1/s1
InChIKeyMRYFMHAPTQCQLE-GOSISDBHSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN1CC(=N[C@@](C)(C1=O)c2cccc(NC(=O)c3ccc(Cl)cn3)c2)N
ACDLabs 12.01Clc1ccc(nc1)C(=O)Nc2cccc(c2)C3(N=C(N)CN(C3=O)C)C
OpenEye OEToolkits 1.7.2C[C@]1(C(=O)N(CC(=N1)N)C)c2cccc(c2)NC(=O)c3ccc(cn3)Cl
OpenEye OEToolkits 1.7.2CC1(C(=O)N(CC(=N1)N)C)c2cccc(c2)NC(=O)c3ccc(cn3)Cl
CACTVS 3.370CN1CC(=N[C](C)(C1=O)c2cccc(NC(=O)c3ccc(Cl)cn3)c2)N
FormulaC18 H18 Cl N5 O2
NameN-{3-[(2R)-6-amino-2,4-dimethyl-3-oxo-2,3,4,5-tetrahydropyrazin-2-yl]phenyl}-5-chloropyridine-2-carboxamide
ChEMBLCHEMBL1923160
DrugBank
ZINCZINC000072318808
PDB chain3u6a Chain A Residue 386 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3u6a Rational design and synthesis of aminopiperazinones as beta-secretase (BACE) inhibitors.
Resolution2.199 Å
Binding residue
(original residue number in PDB)		Q12 G13 L30 D32 Y71 F108 D228 G230 T231 T232
Binding residue
(residue number reindexed from 1)		Q15 G16 L33 D35 Y74 F111 D221 G223 T224 T225
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.49,IC50=0.324uM
BindingDB: IC50=36nM
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:3u6a, PDBe:3u6a, PDBj:3u6a
PDBsum3u6a
PubMed22071305
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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