Structure of PDB 3tmk Chain F Binding Site BS01

Receptor Information
>3tmk Chain F (length=216) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLIN
EYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGV
AYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDER
YETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIV
EPVLSTHIDHDKFSFF
Ligand information
Ligand IDT5A
InChIInChI=1S/C20H30N7O23P5/c1-8-3-26(20(32)25-18(8)31)12-2-9(28)10(45-12)4-43-51(33,34)47-53(37,38)49-55(41,42)50-54(39,40)48-52(35,36)44-5-11-14(29)15(30)19(46-11)27-7-24-13-16(21)22-6-23-17(13)27/h3,6-7,9-12,14-15,19,28-30H,2,4-5H2,1H3,(H,33,34)(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H2,21,22,23)(H,25,31,32)/t9-,10+,11+,12+,14+,15+,19+/m0/s1
InChIKeyJCFDSPQTEMXXLO-SLFMBYJQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O
FormulaC20 H30 N7 O23 P5
NameP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
ChEMBLCHEMBL1236157
DrugBankDB03280
ZINCZINC000169331553
PDB chain3tmk Chain F Residue 217 [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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PDB3tmk Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-thymidyl) pentaphosphate (TP5A) at 2.0 A resolution: implications for catalysis and AZT activation.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D14 R15 T16 G17 K18 T19 T20 K37 F38 P39 R41 L53 F69 R73 R94 G99 Y102 K143 Y151 K187 G188 I189
Binding residue
(residue number reindexed from 1)		D14 R15 T16 G17 K18 T19 T20 K37 F38 P39 R41 L53 F69 R73 R94 G99 Y102 K143 Y151 K187 G188 I189
Annotation score3
Binding affinityMOAD: Kd=135nM
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3tmk, PDBe:3tmk, PDBj:3tmk
PDBsum3tmk
PubMed9521686
UniProtP00572|KTHY_YEAST Thymidylate kinase (Gene Name=CDC8)

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