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Receptor Information

>3qx3 Chain B (length=671) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYG
VFPLRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLR
YGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPAKEAKE
YFADMERHRILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRR
LHGTKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKR
NDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQP
IGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQRV
EPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPH
PMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVYK
EQVLEPMLNGPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFK
LQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGM
LGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAW
KEAQGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLW
KEDLAAFVEELDKVESQERED

Ligand ID

EVP

InChI

InChI=1S/C29H32O13/c1-11-36-9-20-27(40-11)24(31)25(32)29(41-20)42-26-14-7-17-16(38-10-39-17)6-13(14)21(22-15(26)8-37-28(22)33)12-4-18(34-2)23(30)19(5-12)35-3/h4-7,11,15,20-22,24-27,29-32H,8-10H2,1-3H3/t11-,15+,20-,21-,22+,24-,25-,26-,27-,29+/m1/s1

InChIKey

VJJPUSNTGOMMGY-MRVIYFEKSA-N

SMILES

Software	SMILES
CACTVS 3.370	COc1cc(cc(OC)c1O)[C@H]2[C@@H]3[C@H](COC3=O)[C@H](O[C@@H]4O[C@@H]5CO[C@@H](C)O[C@H]5[C@H](O)[C@H]4O)c6cc7OCOc7cc26
OpenEye OEToolkits 1.7.2	CC1OCC2C(O1)C(C(C(O2)OC3c4cc5c(cc4C(C6C3COC6=O)c7cc(c(c(c7)OC)O)OC)OCO5)O)O
OpenEye OEToolkits 1.7.2	C[C@@H]1OC[C@@H]2[C@@H](O1)[C@@H]([C@H]([C@@H](O2)O[C@@H]3c4cc5c(cc4[C@H]([C@@H]6[C@@H]3COC6=O)c7cc(c(c(c7)OC)O)OC)OCO5)O)O
ACDLabs 12.01	O=C1OCC7C1C(c2cc(OC)c(O)c(OC)c2)c4cc3OCOc3cc4C7OC6OC5C(OC(OC5)C)C(O)C6O
CACTVS 3.370	COc1cc(cc(OC)c1O)[CH]2[CH]3[CH](COC3=O)[CH](O[CH]4O[CH]5CO[CH](C)O[CH]5[CH](O)[CH]4O)c6cc7OCOc7cc26

Formula

C29 H32 O13

Name

(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside;
Etoposide;
VP-16

PDB chain

3qx3 Chain D Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3qx3 Structural basis of type II topoisomerase inhibition by the anticancer drug etoposide
Resolution	2.162 Å
Binding residue (original residue number in PDB)	G478 D479 R503 M782
Binding residue (residue number reindexed from 1)	G30 D31 R55 M280
Annotation score	1
Binding affinity	BindingDB: IC50=70nM,EC50=>70000nM

Enzyme Commision number

5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).

	Molecular Function
GO:0003677	DNA binding
GO:0003918	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524	ATP binding

	Biological Process
GO:0006259	DNA metabolic process
GO:0006265	DNA topological change

PDB	RCSB:3qx3, PDBe:3qx3, PDBj:3qx3
PDBsum	3qx3
PubMed	21778401
UniProt	Q02880\|TOP2B_HUMAN DNA topoisomerase 2-beta (Gene Name=TOP2B)

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Structure of PDB 3qx3 Chain B Binding Site BS05