Structure of PDB 5yls Chain A Binding Site BS03

Receptor Information
>5yls 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 IDY50
InChIInChI=1S/C22H23NO4/c1-22(2)12-11-16-19(25-3)10-7-15(21(16)27-22)18(24)8-5-14-6-9-20(26-4)17(23)13-14/h5-13H,23H2,1-4H3/b8-5+
InChIKeyIUIOXMRMRADSKI-VMPITWQZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(/C=C/C(=O)c2ccc(OC)c3C=CC(C)(C)Oc23)cc1N
OpenEye OEToolkits 2.0.6CC1(C=Cc2c(ccc(c2O1)C(=O)C=Cc3ccc(c(c3)N)OC)OC)C
CACTVS 3.385COc1ccc(C=CC(=O)c2ccc(OC)c3C=CC(C)(C)Oc23)cc1N
OpenEye OEToolkits 2.0.6CC1(C=Cc2c(ccc(c2O1)C(=O)/C=C/c3ccc(c(c3)N)OC)OC)C
FormulaC22 H23 N O4
NameE-3-(3-azanyl-4-methoxy-phenyl)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)prop-2-en-1-one
ChEMBLCHEMBL3338195
DrugBank
ZINCZINC000205663719
PDB chain5yls Chain B Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5yls The compound millepachine and its derivatives inhibit tubulin polymerization by irreversibly binding to the colchicine-binding site in beta-tubulin.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		A180 V181
Binding residue
(residue number reindexed from 1)		A180 V181
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.29,Kd=5.13uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yls, PDBe:5yls, PDBj:5yls
PDBsum5yls
PubMed29691282
UniProtQ2XVP4|TBA1B_PIG Tubulin alpha-1B chain (Gene Name=TUBA1B)

[Back to BioLiP]