Structure of PDB 6yv2 Chain A Binding Site BS01

Receptor Information
>6yv2 Chain A (length=358) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCD
SRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDV
WSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTG
VLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAP
TEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQW
LFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACL
SHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHTPLKGCPVHLVDSCPWPH
CNPSCPTG
Ligand information
Ligand IDPUE
InChIInChI=1S/C11H13NO2/c13-11(14)9-6-7-12(8-9)10-4-2-1-3-5-10/h1-5,9H,6-8H2,(H,13,14)/t9-/m1/s1
InChIKeyIOFLKIRLUFZCHR-SECBINFHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)N2CCC(C2)C(=O)O
CACTVS 3.385OC(=O)[CH]1CCN(C1)c2ccccc2
CACTVS 3.385OC(=O)[C@@H]1CCN(C1)c2ccccc2
OpenEye OEToolkits 2.0.7c1ccc(cc1)N2CC[C@H](C2)C(=O)O
FormulaC11 H13 N O2
Name(3~{R})-1-phenylpyrrolidine-3-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000020357882
PDB chain6yv2 Chain A Residue 502 [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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PDB6yv2 Screening of a Custom-Designed Acid Fragment Library Identifies 1-Phenylpyrroles and 1-Phenylpyrrolidines as Inhibitors of Notum Carboxylesterase Activity.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		W128 Y129 S232 A233 F268 I291 F319 A342
Binding residue
(residue number reindexed from 1)		W41 Y42 S145 A146 F181 I204 F232 A255
Annotation score1
Binding affinityMOAD: ic50=48uM
BindingDB: IC50=48000nM
Enzymatic activity
Enzyme Commision number 3.1.1.98: [Wnt protein] O-palmitoleoyl-L-serine hydrolase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity

View graph for
Molecular Function
External links
PDB RCSB:6yv2, PDBe:6yv2, PDBj:6yv2
PDBsum6yv2
PubMed32787107
UniProtQ6P988|NOTUM_HUMAN Palmitoleoyl-protein carboxylesterase NOTUM (Gene Name=NOTUM)

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