Structure of PDB 3w8r Chain A Binding Site BS01

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 IDCTN
InChIInChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
InChIKeyUHDGCWIWMRVCDJ-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)CO
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)O
FormulaC9 H13 N3 O5
Name4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE;
CYTIDINE
ChEMBLCHEMBL95606
DrugBankDB02097
ZINCZINC000002583632
PDB chain3w8r Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3w8r Indispensable residue for uridine binding in the uridine-cytidine kinase family.
Resolution2.5 Å
Binding residue
(original residue number in PDB)
D40 Y43 Y59 D60 Y88 R142 R152 Q160
Binding residue
(residue number reindexed from 1)
D36 Y39 Y55 D56 Y84 R138 R148 Q156
Annotation score5
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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:3w8r, PDBe:3w8r, PDBj:3w8r
PDBsum3w8r
PubMed28955773
UniProtQ5SKR5|URK_THET8 Uridine kinase (Gene Name=udk)

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