Structure of PDB 3zki Chain A Binding Site BS01

Receptor Information
>3zki Chain A (length=365) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSY
IDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLV
NIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIP
NVFSMQMCGAGNGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEI
GGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIFSDG
FWTGSQLACWTPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMYECY
RFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEI
SGPFSTEDVASNCVP
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 chain3zki Chain A Residue 1398 [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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PDB3zki Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G27 R28 G29 L46 D48 Y87 W131 I134 D241 G243 T244 T245 A347
Binding residue
(residue number reindexed from 1)		G14 R15 G16 L33 D35 Y74 W118 I121 D220 G222 T223 T224 A315
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.92,IC50=1.2uM
Enzymatic activity
Catalytic site (original residue number in PDB) D48 S51 N53 A55 Y87 D241 T244
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 D220 T223
Enzyme Commision number 3.4.23.45: memapsin 1.
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:3zki, PDBe:3zki, PDBj:3zki
PDBsum3zki
PubMed23695257
UniProtQ9Y5Z0|BACE2_HUMAN Beta-secretase 2 (Gene Name=BACE2)

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