Structure of PDB 6f25 Chain B Binding Site BS01

Receptor Information
>6f25 Chain B (length=535) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DAELLVTVRGGRLRGIRLKTPGGPVSAFLGIPFAEPPMGPRRFLPPEPKQ
PWSGVVDATTFQSVCYQYVDTLYPGFEGTEMWNPNRELSEDCLYLNVWTP
YPRPTSPTPVLVWIYGGGFYSGASSLDVYDGRFLVQAERTVLVSMNYRVG
AFGFLALPGSREAPGNVGLLDQRLALQWVQENVAAFGGDPTSVTLFGESA
GAASVGMHLLSPPSRGLFHRAVLQSGAPNGPWATVGMGEARRRATQLAHL
VGCPPGNDTELVACLRTRPAQVLVNHEWHVLPQESVFRFSFVPVVDGDFL
SDTPEALINAGDFHGLQVLVGVVKDEGSYFLVYGAPGFSKDNESLISRAE
FLAGVRVGVPQVSDLAAEAVVLHYTDWLHPEDPARLREALSDVVGDHNVV
CPVAQLAGRLAAQGARVYAYVFEHRASTLSWPLWMGVPHGYEIEFIFGIP
LDPSRNYTAEEKIFAQRLMRYWANFARTGDPNEPRDPKAPQWPPYTAGAQ
QYVSLDLRPLEVRRGLRAQACAFWNRFLPKLLSAT
Ligand information
Ligand IDCVZ
InChIInChI=1S/C33H44N6O6/c1-4-34(25-28-16-8-10-18-30(28)38(42)43)20-12-6-14-22-36-27(3)24-32(40)37(33(36)41)23-15-7-13-21-35(5-2)26-29-17-9-11-19-31(29)39(44)45/h8-11,15-19,23-24H,4-7,12-14,20-22,25-26H2,1-3H3/b23-15+
InChIKeyWVBROKGEXVFXBW-HZHRSRAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCN(CCCCCN1C(=CC(=O)N(C1=O)C=CCCCN(CC)Cc2ccccc2[N+](=O)[O-])C)Cc3ccccc3[N+](=O)[O-]
OpenEye OEToolkits 2.0.6CCN(CCCCCN1C(=CC(=O)N(C1=O)/C=C/CCCN(CC)Cc2ccccc2[N+](=O)[O-])C)Cc3ccccc3[N+](=O)[O-]
CACTVS 3.385CCN(CCCCCN1C(=CC(=O)N(\C=C\CCCN(CC)Cc2ccccc2[N+]([O-])=O)C1=O)C)Cc3ccccc3[N+]([O-])=O
CACTVS 3.385CCN(CCCCCN1C(=CC(=O)N(C=CCCCN(CC)Cc2ccccc2[N+]([O-])=O)C1=O)C)Cc3ccccc3[N+]([O-])=O
FormulaC33 H44 N6 O6
Name3-[(~{E})-5-[ethyl-[(2-nitrophenyl)methyl]amino]pent-1-enyl]-1-[5-[ethyl-[(2-nitrophenyl)methyl]amino]pentyl]-6-methyl-pyrimidine-2,4-dione
ChEMBL
DrugBank
ZINC
PDB chain6f25 Chain B Residue 610 [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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PDB6f25 New evidence for dual binding site inhibitors of acetylcholinesterase as improved drugs for treatment of Alzheimer's disease.
Resolution3.052 Å
Binding residue
(original residue number in PDB)		W86 G121 Y124 S203 W286 H287 Q291 E292 Y337 F338 Y341 H447
Binding residue
(residue number reindexed from 1)		W82 G117 Y120 S199 W278 H279 Q283 E284 Y329 F330 Y333 H439
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G121 G122 G154 S203 A204 G242 F297 F299 E334 H447
Catalytic site (residue number reindexed from 1) G117 G118 G150 S199 A200 G238 F289 F291 E326 H439
Enzyme Commision number 3.1.1.7: acetylcholinesterase.
Gene Ontology
Molecular Function
GO:0001540 amyloid-beta binding
GO:0003990 acetylcholinesterase activity
GO:0004104 cholinesterase activity
GO:0005515 protein binding
GO:0005518 collagen binding
GO:0016787 hydrolase activity
GO:0017171 serine hydrolase activity
GO:0042166 acetylcholine binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0043236 laminin binding
GO:0052689 carboxylic ester hydrolase activity
Biological Process
GO:0001507 acetylcholine catabolic process in synaptic cleft
GO:0001919 regulation of receptor recycling
GO:0002076 osteoblast development
GO:0006581 acetylcholine catabolic process
GO:0007155 cell adhesion
GO:0007399 nervous system development
GO:0007416 synapse assembly
GO:0031623 receptor internalization
GO:0032223 negative regulation of synaptic transmission, cholinergic
GO:0042982 amyloid precursor protein metabolic process
GO:0050714 positive regulation of protein secretion
GO:0060041 retina development in camera-type eye
GO:0095500 acetylcholine receptor signaling pathway
GO:0120162 positive regulation of cold-induced thermogenesis
Cellular Component
GO:0005576 extracellular region
GO:0005604 basement membrane
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0031594 neuromuscular junction
GO:0043083 synaptic cleft
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0098552 side of membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6f25, PDBe:6f25, PDBj:6f25
PDBsum6f25
PubMed31132435
UniProtP22303|ACES_HUMAN Acetylcholinesterase (Gene Name=ACHE)

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