Structure of PDB 3zov Chain A Binding Site BS01

Receptor Information
>3zov Chain A (length=371) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPH
PFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTV
RANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTH
VPNLFSLQLCGSVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVE
INGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVASIKAASSTEKF
PDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLR
PVEDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDE
FRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDWZV
InChIInChI=1S/C20H20F3N5O3/c1-19(9-16(29)28(2)18(24)27-19)12-4-3-5-13(8-12)26-17(30)15-7-6-14(10-25-15)31-11-20(21,22)23/h3-8,10H,9,11H2,1-2H3,(H2,24,27)(H,26,30)/t19-/m0/s1
InChIKeyZJFIBYCNZHIVEL-IBGZPJMESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=N[C](C)(CC1=O)c2cccc(NC(=O)c3ccc(OCC(F)(F)F)cn3)c2)N
CACTVS 3.385CN1C(=N[C@@](C)(CC1=O)c2cccc(NC(=O)c3ccc(OCC(F)(F)F)cn3)c2)N
ACDLabs 12.01O=C3N(C(=NC(c2cccc(NC(=O)c1ncc(OCC(F)(F)F)cc1)c2)(C)C3)N)C
OpenEye OEToolkits 1.9.2C[C@]1(CC(=O)N(C(=N1)N)C)c2cccc(c2)NC(=O)c3ccc(cn3)OCC(F)(F)F
OpenEye OEToolkits 1.9.2CC1(CC(=O)N(C(=N1)N)C)c2cccc(c2)NC(=O)c3ccc(cn3)OCC(F)(F)F
FormulaC20 H20 F3 N5 O3
Name5-(2,2,2-Trifluoro-ethoxy)-pyridine-2-carboxylic acid [3-((S)-2-amino-1,4-dimethyl-6-oxo-1,4,5,6-tetrahydro-pyrimidin-4-yl)-phenyl]-amide
ChEMBL
DrugBank
ZINCZINC000095920556
PDB chain3zov Chain A Residue 1447 [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]
PDB3zov Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G72 Q73 G74 Y75 L91 D93 Y132 F169 D289 G291 T293 A396
Binding residue
(residue number reindexed from 1)		G16 Q17 G18 Y19 L35 D37 Y76 F113 D221 G223 T225 A321
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.22,IC50=0.06uM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D37 S40 N42 A44 Y76 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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3zov, PDBe:3zov, PDBj:3zov
PDBsum3zov
PubMed23695257
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]