Structure of PDB 4tmk Chain A Binding Site BS01

Receptor Information
>4tmk Chain A (length=210) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSKYIVIEGLEGAGKTTARNVVVETLEQLGIRDMVFTREPGGTQLAEKLR
SLLLDIKSVGDEVITDKAEVLMFYAARVQLVETVIKPALANGTWVIGDRH
DLSTQAYQGGGRGIDQHMLATLRDAVLGDFRPDLTLYLDVTPEVGLKRAR
ARGELDRIEQESFDFFNRTRARYLELAAQDKSIHTIDATQPLEAVMDAIR
TTVTHWVKEL
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 chain4tmk Chain A Residue 214 [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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PDB4tmk Structural basis for efficient phosphorylation of 3'-azidothymidine monophosphate by Escherichia coli thymidylate kinase.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		E12 G13 G15 K16 T17 R39 E40 L55 F74 R78 R100 S104 T105 Y108 Q109 R149 R153 I159
Binding residue
(residue number reindexed from 1)		E11 G12 G14 K15 T16 R38 E39 L54 F73 R77 R99 S103 T104 Y107 Q108 R148 R152 I158
Annotation score3
Binding affinityMOAD: Kd=20nM
PDBbind-CN: -logKd/Ki=7.70,Kd=20nM
Enzymatic activity
Enzyme Commision number 2.7.4.9: dTMP kinase.
Gene Ontology
Molecular Function
GO:0004798 thymidylate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0006227 dUDP biosynthetic process
GO:0006233 dTDP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0009165 nucleotide biosynthetic process
GO:0015949 nucleobase-containing small molecule interconversion
GO:0016310 phosphorylation
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4tmk, PDBe:4tmk, PDBj:4tmk
PDBsum4tmk
PubMed9826650
UniProtP0A720|KTHY_ECOLI Thymidylate kinase (Gene Name=tmk)

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