Structure of PDB 1mw8 Chain X Binding Site BS02

Receptor Information
>1mw8 Chain X (length=561) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGDERGALVNRM
GVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAW
HLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFM
DRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWE
VDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLER
EDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMR
TDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASEAREAIRPSDVNVM
AESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARG
RILRFDGWTKVMPAEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEAS
LVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLE
ENFRELMNYDFTAQMENNLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKD
PEEGGMRPNQM
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 chain1mw8 Chain X Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1mw8 Structure of a Complex between E. coli DNA Topoisomerase I and Single-Stranded DNA.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D113 R114 E115 R161 R168 R365 S495
Binding residue
(residue number reindexed from 1)		D92 R93 E94 R140 R147 R339 S464
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E9 S10 D113 E115 Y319 R321
Catalytic site (residue number reindexed from 1) E8 S9 D92 E94 Y298 R300
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1mw8, PDBe:1mw8, PDBj:1mw8
PDBsum1mw8
PubMed14604525
UniProtP06612|TOP1_ECOLI DNA topoisomerase 1 (Gene Name=topA)

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