Structure of PDB 5yls Chain B Binding Site BS02

Receptor Information
>5yls Chain B (length=428) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVY
YNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNN
WAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTL
LISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETY
CIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADL
RKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVK
TAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG
EGMDEMEFTEAESNMNDLVSEYQQYQDA
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
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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)		V236 C239 A248 D249 L253 N256 M257 T312 N348 K350 A352
Binding residue
(residue number reindexed from 1)		V236 C239 A248 D249 L253 N256 M257 T312 N348 K350 A352
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.29,Kd=5.13uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005200 structural constituent of cytoskeleton
GO:0005515 protein binding
GO:0005525 GTP binding
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yls, PDBe:5yls, PDBj:5yls
PDBsum5yls
PubMed29691282
UniProtP02554|TBB_PIG Tubulin beta chain

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