Structure of PDB 5nn0 Chain A Binding Site BS03

Receptor Information
>5nn0 Chain A (length=527) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKW
SDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAP
KPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALG
FLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAA
SVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGC
SRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDM
PDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQE
GLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPA
LEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLER
RDQYTKAEEILSRSIVKRWANFAKYGNPQETQNNSTSWPVFKSTEQKYLT
LNTESTRIMTKLRAQQCRFWTSFFPKV
Ligand information
Ligand ID92H
InChIInChI=1S/C30H37N3O/c1-31(2)16-17-33(30(34)28-14-13-24-9-3-4-10-25(24)18-28)22-23-8-7-15-32(21-23)29-19-26-11-5-6-12-27(26)20-29/h3-6,9-14,18,23,29H,7-8,15-17,19-22H2,1-2H3/t23-/m1/s1
InChIKeyOFDHKZMZEXORRX-HSZRJFAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN(C)CCN(CC1CCCN(C1)C2Cc3ccccc3C2)C(=O)c4ccc5ccccc5c4
CACTVS 3.385
OpenEye OEToolkits 2.0.6		CN(C)CCN(C[C@@H]1CCCN(C1)C2Cc3ccccc3C2)C(=O)c4ccc5ccccc5c4
CACTVS 3.385CN(C)CCN(C[CH]1CCCN(C1)C2Cc3ccccc3C2)C(=O)c4ccc5ccccc5c4
FormulaC30 H37 N3 O
Name~{N}-[[(3~{R})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-3-yl]methyl]-~{N}-[2-(dimethylamino)ethyl]naphthalene-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain5nn0 Chain A Residue 626 [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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PDB5nn0 The Magic of Crystal Structure-Based Inhibitor Optimization: Development of a Butyrylcholinesterase Inhibitor with Picomolar Affinity and in Vivo Activity.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		L236 V294 G296 M302
Binding residue
(residue number reindexed from 1)		L234 V292 G294 M300
Annotation score1
Binding affinityMOAD: Kd=11.1pM
PDBbind-CN: -logKd/Ki=10.96,Kd=11pM
BindingDB: IC50=1.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) G116 G117 G149 S198 A199 Y237 V288 F290 E325 H438
Catalytic site (residue number reindexed from 1) G114 G115 G147 S196 A197 Y235 V286 F288 E323 H436
Enzyme Commision number 3.1.1.8: cholinesterase.
Gene Ontology
Molecular Function
GO:0001540 amyloid-beta binding
GO:0003824 catalytic activity
GO:0003990 acetylcholinesterase activity
GO:0004104 cholinesterase activity
GO:0005515 protein binding
GO:0016788 hydrolase activity, acting on ester bonds
GO:0019899 enzyme binding
GO:0033265 choline binding
GO:0042802 identical protein binding
GO:0052689 carboxylic ester hydrolase activity
Biological Process
GO:0006581 acetylcholine catabolic process
GO:0006805 xenobiotic metabolic process
GO:0007584 response to nutrient
GO:0007612 learning
GO:0008285 negative regulation of cell population proliferation
GO:0009410 response to xenobiotic stimulus
GO:0014016 neuroblast differentiation
GO:0016486 peptide hormone processing
GO:0019695 choline metabolic process
GO:0043279 response to alkaloid
GO:0050783 cocaine metabolic process
GO:0050805 negative regulation of synaptic transmission
GO:0051384 response to glucocorticoid
GO:0051593 response to folic acid
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005641 nuclear envelope lumen
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0005886 plasma membrane
GO:0072562 blood microparticle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5nn0, PDBe:5nn0, PDBj:5nn0
PDBsum5nn0
PubMed29227101
UniProtP06276|CHLE_HUMAN Cholinesterase (Gene Name=BCHE)

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