Structure of PDB 5yl2 Chain B Binding Site BS02

Receptor Information
>5yl2 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 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)		V236 C239 L246 A248 D249 L253 N256 M257 N348 K350 A352
Binding residue
(residue number reindexed from 1)		V236 C239 L246 A248 D249 L253 N256 M257 N348 K350 A352
Annotation score1
Binding affinityMOAD: Kd=31.69uM
PDBbind-CN: -logKd/Ki=4.50,Kd=31.69uM
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
View graph for
Cellular Component
External links
PDB RCSB:5yl2, PDBe:5yl2, PDBj:5yl2
PDBsum5yl2
PubMed29691282
UniProtP02554|TBB_PIG Tubulin beta chain

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