Structure of PDB 5xlt Chain B Binding Site BS02

Receptor Information
>5xlt Chain B (length=427) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYY
NEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNW
AKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLL
ISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYC
IDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLR
KLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMA
ACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKT
AVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGE
GMDEMEFTEAESNMNDLVSEYQQYQDA
Ligand information
Ligand ID89O
InChIInChI=1S/C21H20O8/c1-25-15-3-9(4-16(26-2)20(15)23)17-10-5-13-14(29-8-28-13)6-11(10)19(22)12-7-27-21(24)18(12)17/h3-6,12,17-19,22-23H,7-8H2,1-2H3/t12-,17+,18-,19+/m0/s1
InChIKeyYVCVYCSAAZQOJI-JHQYFNNDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COc1cc(cc(c1O)OC)[C@@H]2c3cc4c(cc3[C@H]([C@@H]5[C@@H]2C(=O)OC5)O)OCO4
CACTVS 3.385COc1cc(cc(OC)c1O)[CH]2[CH]3[CH](COC3=O)[CH](O)c4cc5OCOc5cc24
OpenEye OEToolkits 2.0.6COc1cc(cc(c1O)OC)C2c3cc4c(cc3C(C5C2C(=O)OC5)O)OCO4
CACTVS 3.385COc1cc(cc(OC)c1O)[C@H]2[C@@H]3[C@H](COC3=O)[C@H](O)c4cc5OCOc5cc24
FormulaC21 H20 O8
Name(5S,5aR,8aR,9R)-9-(3,5-dimethoxy-4-oxidanyl-phenyl)-5-oxidanyl-5a,6,8a,9-tetrahydro-5H-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one
ChEMBLCHEMBL31929
DrugBank
ZINCZINC000005670074
PDB chain5xlt Chain B Residue 505 [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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PDB5xlt Structure of 4'-demethylepipodophyllotoxin in complex with tubulin provides a rationale for drug design
Resolution2.813 Å
Binding residue
(original residue number in PDB)		V236 C239 L240 A248 D249 K252 L253 N256 M257 V313 N348 K350 A352
Binding residue
(residue number reindexed from 1)		V235 C238 L239 A247 D248 K251 L252 N255 M256 V312 N347 K349 A351
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005200 structural constituent of cytoskeleton
GO:0005525 GTP binding
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity
Biological Process
GO:0000226 microtubule cytoskeleton organization
GO:0000278 mitotic cell cycle
GO:0007017 microtubule-based process
GO:0007399 nervous system development
GO:1902669 positive regulation of axon guidance
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:5xlt, PDBe:5xlt, PDBj:5xlt
PDBsum5xlt
PubMed28864414
UniProtQ6B856|TBB2B_BOVIN Tubulin beta-2B chain (Gene Name=TUBB2B)

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