Structure of PDB 8j9v Chain B Binding Site BS04

Receptor Information
>8j9v Chain B (length=778) Species: 10497 (African swine fever virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDKYTRARNAGGKRAQDCMLLAAEGDSALSLLRTGLTLGKSNPSGPSFDF
CGMISLGGVIMNACKKVTNITTDSGETIMVRNEQLTNNKVLQGIVQVLGL
DFNCHYKTQEERAKLRYGCIVACVDQDLDGCGKILGLLLAYFHLFWPQLI
IHGFVKRLLTPLIRVYEKGKTMPVEFYYEQEFDAWAKKQTSLVNHTVKYY
KGLAAHDTHEVKSMFKHFDNMVYTFTLDDSAKELFHIYFGGESELRKREL
CTGVVPLTETQTQSIHSVRRIPCSLHLQVDTKAYKLDAIERQIPNFLDGM
TRARRKILAGGVKCFASNNRERKVFQFGGYVADHMFYHHGDMSLNTSIIK
AAQYYPGSSHLYPVFIGIGSFGSRHLGGKDAGSPRYISVQLASEFIKTMF
PAEDSWLLPYVFEDGQRAEPEYYVPVLPLAIMEYGANPSEGWKYTTWARQ
LEDILALVRAYVDKDNPKHELLHYAIKHKITILPLRPSNYNFKGHLKRFG
QYYYSYGTYDISEQRNIITITELPLRVPTVAYIESIKKSSNRMTFIEEII
DYSSSETIEILVKLKPNSLNRIVEEFKETEEQDSIENFLRLRNCLHSHLN
FVKPKGGIIEFNSYYEILYAWLPYRRELYQKRLMREHAVLKLRIIMETAI
VRYINESAELNLSHYEDEKEASRILSEHGFPPLNHTLIISPEFASIEELN
QKALQGCYTYILSLQARELLIAAKTRRVEKIKKMQARLDKVEQLLQESPF
PGASVWLEEIDAVEKAIIKGRNTQWKFH
Ligand information
Ligand IDEVP
InChIInChI=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
InChIKeyVJJPUSNTGOMMGY-MRVIYFEKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370COc1cc(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 1.7.2CC1OCC2C(O1)C(C(C(O2)OC3c4cc5c(cc4C(C6C3COC6=O)c7cc(c(c(c7)OC)O)OC)OCO5)O)O
OpenEye OEToolkits 1.7.2C[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 12.01O=C1OCC7C1C(c2cc(OC)c(O)c(OC)c2)c4cc3OCOc3cc4C7OC6OC5C(OC(OC5)C)C(O)C6O
CACTVS 3.370COc1cc(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
FormulaC29 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
ChEMBLCHEMBL44657
DrugBankDB00773
ZINCZINC000003938684
PDB chain8j9v Chain F Residue 101 [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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PDB8j9v Cryo-EM structure of the African swine fever virus topoisomerase 2 complexed with Cut02aDNA and etoposide (EDI-1)
Resolution2.71 Å
Binding residue
(original residue number in PDB)		E438 G439 D440 M756 T760
Binding residue
(residue number reindexed from 1)		E24 G25 D26 M342 T346
Annotation score1
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003916 DNA topoisomerase activity
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0000819 sister chromatid segregation
GO:0006259 DNA metabolic process
GO:0006265 DNA topological change
Cellular Component
GO:0030430 host cell cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8j9v, PDBe:8j9v, PDBj:8j9v
PDBsum8j9v
PubMed38418525
UniProtQ00942|TOP2_ASFB7 DNA topoisomerase 2 (Gene Name=TOP)

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