Structure of PDB 3zkn Chain B Binding Site BS01

Receptor Information
>3zkn Chain B (length=375) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSY
IDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLV
NIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIP
NVFSMQMCGANGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIG
GQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSD
GFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPM
MGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCA
EIAGAAVSEISGPFSTEDVASNCVP
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 chain3zkn Chain B Residue 1398 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3zkn Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D48 Y87 Q89 N123 L126 I134 D241
Binding residue
(residue number reindexed from 1)		D35 Y74 Q76 N110 L113 I121 D219
Annotation score1
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 D219 T222
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:3zkn, PDBe:3zkn, PDBj:3zkn
PDBsum3zkn
PubMed23695257
UniProtQ9Y5Z0|BACE2_HUMAN Beta-secretase 2 (Gene Name=BACE2)

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