Structure of PDB 3l4k Chain A Binding Site BS08

Receptor Information
>3l4k Chain A (length=721) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYG
CYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGH
LMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITK
PTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNL
DRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEI
PISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELK
VAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTR
ATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLP
ILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFR
GWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGL
SGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPI
SLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEV
EKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGS
EELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWN
TDLKAFEVGYQEFLQRDAEAR
Ligand information
Ligand IDTSP
InChIInChI=1S/C10H15N2O7PS/c1-5-3-12(10(14)11-9(5)13)8-2-7(21)6(19-8)4-18-20(15,16)17/h3,6-8,21H,2,4H2,1H3,(H,11,13,14)(H2,15,16,17)/t6-,7+,8-/m1/s1
InChIKeyBORVFKJZAOEGOO-GJMOJQLCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01P(=O)(O)(O)OCC1OC(CC1S)N2C(=O)NC(=O)C(C)=C2
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)S
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)S
CACTVS 3.385CC1=CN([CH]2C[CH](S)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.385CC1=CN([C@H]2C[C@H](S)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H15 N2 O7 P S
Name3'-THIO-THYMIDINE-5'-PHOSPHATE
ChEMBL
DrugBankDB08651
ZINCZINC000033516765
PDB chain3l4k Chain D Residue 11 [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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PDB3l4k A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.
Resolution2.98 Å
Binding residue
(original residue number in PDB)		E449 D530 H736
Binding residue
(residue number reindexed from 1)		E29 D110 H316
Annotation score1
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3l4k, PDBe:3l4k, PDBj:3l4k
PDBsum3l4k
PubMed20485342
UniProtP06786|TOP2_YEAST DNA topoisomerase 2 (Gene Name=TOP2)

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