Structure of PDB 5zb0 Chain A Binding Site BS01

Receptor Information
>5zb0 Chain A (length=187) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PGLFLTLEGLDGSGKTTQARRLAAFLEAQGRPVLLTREPGGGLPEVRSLL
LTQELSPEAEYLLFSADRAEHVRKVILPGLAAGKVVISDRYLDSSLAYQG
YGRGLPLPWLREVAREATRGLKPRLTFLLDLPPEAALEGLGLEFFRRVRE
GYLALARAEPGRFVVLDATLPEEEIARAIQAHLRPLL
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 chain5zb0 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5zb0 Insights into product release dynamics through structural analyses of thymidylate kinase.
Resolution1.19 Å
Binding residue
(original residue number in PDB)		D12 R38 E39 P40 R48 F65 R69 R91 S95 S96 Y99 Q100
Binding residue
(residue number reindexed from 1)		D11 R37 E38 P39 R47 F64 R68 R90 S94 S95 Y98 Q99
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5zb0, PDBe:5zb0, PDBj:5zb0
PDBsum5zb0
PubMed30447376
UniProtQ5SHX3|KTHY_THET8 Thymidylate kinase (Gene Name=tmk)

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