Structure of PDB 5yl2 Chain A Binding Site BS03

Receptor Information
>5yl2 Chain A (length=437) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFN
TFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAA
NNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFT
SLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDC
AFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNV
DLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTG
FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA
KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGV
Ligand information
Ligand ID8WU
InChIInChI=1S/C22H22O5/c1-22(2)12-11-16-19(25-3)10-7-15(21(16)27-22)17(23)8-5-14-6-9-20(26-4)18(24)13-14/h5-13,24H,1-4H3/b8-5+
InChIKeyXJMCEQUUSGXSES-VMPITWQZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1(C=Cc2c(ccc(c2O1)C(=O)/C=C/c3ccc(c(c3)O)OC)OC)C
CACTVS 3.385COc1ccc(C=CC(=O)c2ccc(OC)c3C=CC(C)(C)Oc23)cc1O
OpenEye OEToolkits 2.0.6CC1(C=Cc2c(ccc(c2O1)C(=O)C=Cc3ccc(c(c3)O)OC)OC)C
CACTVS 3.385COc1ccc(/C=C/C(=O)c2ccc(OC)c3C=CC(C)(C)Oc23)cc1O
FormulaC22 H22 O5
Name(E)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)-3-(4-methoxy-3-oxidanyl-phenyl)prop-2-en-1-one
ChEMBLCHEMBL2336890
DrugBank
ZINCZINC000095590502
PDB chain5yl2 Chain B Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yl2 The compound millepachine and its derivatives inhibit tubulin polymerization by irreversibly binding to the colchicine-binding site in beta-tubulin.
Resolution2.09 Å
Binding residue
(original residue number in PDB)		T179 A180 V181
Binding residue
(residue number reindexed from 1)		T179 A180 V181
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.50,Kd=31.69uM
Enzymatic activity
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005200 structural constituent of cytoskeleton
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0000226 microtubule cytoskeleton organization
GO:0000278 mitotic cell cycle
GO:0007017 microtubule-based process
Cellular Component
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0015630 microtubule cytoskeleton

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yl2, PDBe:5yl2, PDBj:5yl2
PDBsum5yl2
PubMed29691282
UniProtQ2XVP4|TBA1B_PIG Tubulin alpha-1B chain (Gene Name=TUBA1B)

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