Structure of PDB 5xb2 Chain A Binding Site BS02

Receptor Information
>5xb2 Chain A (length=194) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREIL
LTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQG
YGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKE
FLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLR
Ligand information
Ligand IDTMP
InChIInChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyGYOZYWVXFNDGLU-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
FormulaC10 H15 N2 O8 P
NameTHYMIDINE-5'-PHOSPHATE
ChEMBLCHEMBL394429
DrugBankDB01643
ZINCZINC000001678872
PDB chain5xb2 Chain A Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5xb2 Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate
Resolution2.161 Å
Binding residue
(original residue number in PDB)		D9 E36 R47 F64 R90 T95 Y98 Q99 R145
Binding residue
(residue number reindexed from 1)		D9 E36 R47 F64 R90 T95 Y98 Q99 R145
Annotation score3
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:5xb2, PDBe:5xb2, PDBj:5xb2
PDBsum5xb2
PubMed28627020
UniProtO67099|KTHY_AQUAE Thymidylate kinase (Gene Name=tmk)

[Back to BioLiP]