Structure of PDB 1cy8 Chain A Binding Site BS01

Receptor Information
>1cy8 Chain A (length=563) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPDERGALVNRMGVD
PWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLR
EVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRV
VGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDA
STTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDK
PTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDS
TNLSQDAVNMVRGYISDNFGKKYLPESPNQYAHEAIRPSDVNVMAESLKD
MEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFD
GWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASL
VKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEE
NFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDP
EEGGMRPNQMVLT
Ligand information
Ligand IDT3P
InChIInChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(7(4-13)19-8)20-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyXXYIANZGUOSQHY-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([C@H]2C[C@H](O[P](O)(O)=O)[C@@H](CO)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([CH]2C[CH](O[P](O)(O)=O)[CH](CO)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(OP(=O)(O)O)C2)CO
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)OP(=O)(O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)OP(=O)(O)O
FormulaC10 H15 N2 O8 P
NameTHYMIDINE-3'-PHOSPHATE;
ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE
ChEMBLCHEMBL408119
DrugBank
ZINCZINC000006521315
PDB chain1cy8 Chain A Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1cy8 Protein-nucleotide interactions in E. coli DNA topoisomerase I.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		D113 R114 R161 R168 H365 R493 S495
Binding residue
(residue number reindexed from 1)		D89 R90 R137 R144 H333 R461 S463
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E9 S10 D111 D113 E115 Y319 R321 H365
Catalytic site (residue number reindexed from 1) E8 S9 D87 D89 E91 Y295 R297 H333
Enzyme Commision number 5.6.2.1: DNA topoisomerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003916 DNA topoisomerase activity
GO:0003917 DNA topoisomerase type I (single strand cut, ATP-independent) activity
Biological Process
GO:0006265 DNA topological change

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Molecular Function
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Biological Process
External links
PDB RCSB:1cy8, PDBe:1cy8, PDBj:1cy8
PDBsum1cy8
PubMed10504732
UniProtP06612|TOP1_ECOLI DNA topoisomerase 1 (Gene Name=topA)

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