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Structure of PDB 1cy7 Chain A Binding Site BS01

Receptor Information
>1cy7 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]
GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTDERGALVNRMGV
DPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHL
REVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDR
VVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVD
ASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLERED
KPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTD
STNLSQDAVNMVRGYISDNFGKKYLPESPNQYENSQEAHEAIRPSDVNVM
AESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARG
RILRFDGWTKVMPALILPAVNKGDALTLVELTPAQHFTKPPARFSEASLV
KELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEEN
FRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPE
EGGMRPNQMVLTS
Ligand information
Ligand IDTMP
InChIInChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyGYOZYWVXFNDGLU-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
FormulaC10 H15 N2 O8 P
NameTHYMIDINE-5'-PHOSPHATE
ChEMBLCHEMBL394429
DrugBankDB01643
ZINCZINC000001678872
PDB chain1cy7 Chain A Residue 600 [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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PDB1cy7 Protein-nucleotide interactions in E. coli DNA topoisomerase I.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D113 R114 E115 R161 R168 H365 S495
Binding residue
(residue number reindexed from 1)		D90 R91 E92 R138 R145 H339 S462
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 D88 D90 E92 Y296 R298 H339
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:1cy7, PDBe:1cy7, PDBj:1cy7
PDBsum1cy7
PubMed10504732
UniProtP06612|TOP1_ECOLI DNA topoisomerase 1 (Gene Name=topA)

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