Structure of PDB 2b8t Chain C Binding Site BS02

Receptor Information
>2b8t Chain C (length=199) Species: 134821 (Ureaplasma parvum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDSRTGTSLPS
VEVESAPEILNYIMSNSFNDETKVIGIDEVQFFDDRICEVANILAENGFV
VIISGLDKNFKGEPFGPIAKLFTYADKITKLTAICNECGAEATHSLRKID
GKHADYNDDIVKIGCQEFYSAVCRHHHKVPNRPYLNSNSEEFIKFFKNK
Ligand information
Ligand IDTHM
InChIInChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1
InChIKeyIQFYYKKMVGJFEH-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)CO
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O
FormulaC10 H14 N2 O5
NameTHYMIDINE;
DEOXYTHYMIDINE;
2'-DEOXYTHYMIDINE
ChEMBLCHEMBL52609
DrugBankDB04485
ZINCZINC000000025672
PDB chain2b8t Chain C Residue 6970 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2b8t Structure of the substrate complex of thymidine kinase from Ureaplasma urealyticum and investigations of possible drug targets for the enzyme
Resolution2.0 Å
Binding residue
(original residue number in PDB)		E97 F100 L124 N127 F128 F133 I178 V179 K180 G182 Y187
Binding residue
(residue number reindexed from 1)		E79 F82 L106 N109 F110 F115 I160 V161 K162 G164 Y169
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.21: thymidine kinase.
Gene Ontology
Molecular Function
GO:0004797 thymidine kinase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006259 DNA metabolic process
GO:0009157 deoxyribonucleoside monophosphate biosynthetic process
GO:0016310 phosphorylation
GO:0046104 thymidine metabolic process
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2b8t, PDBe:2b8t, PDBj:2b8t
PDBsum2b8t
PubMed16336273
UniProtQ9PPP5|KITH_UREPA Thymidine kinase (Gene Name=tdk)

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