Structure of PDB 3u6a Chain C Binding Site BS01

Receptor Information
>3u6a Chain C (length=384) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPH
PFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTV
RANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTH
VPNLFSLQLCGAGFPLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEV
IIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAA
SSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITIL
PQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKR
IGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
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 C Residue 386 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3u6a Rational design and synthesis of aminopiperazinones as beta-secretase (BACE) inhibitors.
Resolution2.199 Å
Binding residue
(original residue number in PDB)		Q12 G13 D32 Y71 T72 Q73 F108 D228 G230 T231 T232
Binding residue
(residue number reindexed from 1)		Q17 G18 D37 Y76 T77 Q78 F113 D227 G229 T230 T231
Annotation score1
Binding affinityBindingDB: 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) D37 S40 N42 A44 Y76 D227 T230
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3u6a, PDBe:3u6a, PDBj:3u6a
PDBsum3u6a
PubMed22071305
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]