Structure of PDB 1tmk Chain A Binding Site BS01

Receptor Information
>1tmk Chain A (length=204) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEY
LTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAY
SAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQFGDERYETVKFQEKVKQ
TFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDK
FSFF
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 chain1tmk Chain A Residue 217 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1tmk Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		D14 K37 F38 R41 L53 F69 R73 R94 S98 G99 Y102 Y151
Binding residue
(residue number reindexed from 1)		D12 K35 F36 R39 L51 F67 R71 R92 S96 G97 Y100 Y139
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.4.9: dTMP kinase.
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
GO:0004798 thymidylate kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0009041 UMP/dUMP kinase activity
GO:0016301 kinase activity
Biological Process
GO:0006227 dUDP biosynthetic process
GO:0006233 dTDP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0016310 phosphorylation
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1tmk, PDBe:1tmk, PDBj:1tmk
PDBsum1tmk
PubMed9253404
UniProtP00572|KTHY_YEAST Thymidylate kinase (Gene Name=CDC8)

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