Structure of PDB 2tmk Chain A Binding Site BS01

Receptor Information
>2tmk 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 IDATM
InChIInChI=1S/C10H14N5O7P/c1-5-3-15(10(17)12-9(5)16)8-2-6(13-14-11)7(22-8)4-21-23(18,19)20/h3,6-8H,2,4H2,1H3,(H,12,16,17)(H2,18,19,20)/t6-,7+,8+/m0/s1
InChIKeyOIFWQOKDSPDILA-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](N=[N+]=[N-])[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(\N=[N+]=[N-])C2)COP(=O)(O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)N=[N+]=[N-]
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)N=[N+]=[N-]
CACTVS 3.341CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H14 N5 O7 P
Name3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL257695
DrugBankDB03666
ZINCZINC000012503817
PDB chain2tmk 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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PDB2tmk Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D14 K37 F38 P39 F69 R73 R94 G99 Y102 Y151
Binding residue
(residue number reindexed from 1)		D12 K35 F36 P37 F67 R71 R92 G97 Y100 Y139
Annotation score2
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2tmk, PDBe:2tmk, PDBj:2tmk
PDBsum2tmk
PubMed9253404
UniProtP00572|KTHY_YEAST Thymidylate kinase (Gene Name=CDC8)

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