Structure of PDB 3hjn Chain B Binding Site BS02

Receptor Information
>3hjn Chain B (length=184) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFITFEGIDGSGKSTQIQLLAQYLEKRGKKVILKREPGGTETGEKIRKIL
LEEEVTPKAELFLFLASRNLLVTEIKQYLSEGYAVLLDRYTDSSVAYQGF
GRNLGKEIVEELNDFATDGLIPDLTFYIDVDVETALKRNRFEKREFLERV
REGYLVLAREHPERIVVLDGKRSIEEIHRDVVRE
Ligand information
Ligand IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain3hjn Chain B Residue 402 [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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PDB3hjn Crystal structure of thymidylate kinase in complex with dTDP and ADP from Thermotoga maritima
Resolution2.1 Å
Binding residue
(original residue number in PDB)		D9 K13 E36 R47 F64 R68 R89 S93 S94 Y97 Q98 F145
Binding residue
(residue number reindexed from 1)		D9 K13 E36 R47 F64 R68 R89 S93 S94 Y97 Q98 F141
Annotation score4
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
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: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:3hjn, PDBe:3hjn, PDBj:3hjn
PDBsum3hjn
PubMed
UniProtQ9X0I3|KTHY_THEMA Thymidylate kinase (Gene Name=tmk)

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