Structure of PDB 3w8r Chain A Binding Site BS02

Receptor Information
>3w8r Chain A (length=207) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPFVIGIAGGTASGKTTLAQALARTLGERVALLPMDHYYKDLGHLPLEER
LRVNYDHPDAFDLALYLEHAQALLRGLPVEMPVYDFRAHTRSPRRTPVRP
APVVILEGILVLYPKELRDLMDLKVFVDADADERFIRRLKRDVLERGRSL
EGVVAQYLEQVKPMHLHFVEPTKRYADVIVPRGGQNPVALEMLAAKALAR
LARMGAA
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain3w8r Chain A Residue 302 [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]
PDB3w8r Indispensable residue for uridine binding in the uridine-cytidine kinase family.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		T15 A16 S17 G18 K19 T20 T21 R145
Binding residue
(residue number reindexed from 1)		T11 A12 S13 G14 K15 T16 T17 R141
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.1.48: uridine/cytidine kinase.
Gene Ontology
Molecular Function
GO:0004849 uridine kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016773 phosphotransferase activity, alcohol group as acceptor
GO:0016887 ATP hydrolysis activity
GO:0043771 cytidine kinase activity
Biological Process
GO:0008655 pyrimidine-containing compound salvage
GO:0009224 CMP biosynthetic process
GO:0016310 phosphorylation
GO:0044206 UMP salvage
GO:0044211 CTP salvage
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3w8r, PDBe:3w8r, PDBj:3w8r
PDBsum3w8r
PubMed28955773
UniProtQ5SKR5|URK_THET8 Uridine kinase (Gene Name=udk)

[Back to BioLiP]