Structure of PDB 8ooj Chain A Binding Site BS02

Receptor Information
>8ooj Chain A (length=232) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNLTMEQKNG
GNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFER
SVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYL
QATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYL
QEVPILTLDVNEDFKDKYESLVEKVKEFLSTL
Ligand information
Ligand IDVVC
InChIInChI=1S/C11H13N3O4/c1-2-11(6-15)7(16)5-9(18-11)14-4-3-8(12)13-10(14)17/h1,3-4,7,9,15-16H,5-6H2,(H2,12,13,17)/t7-,9+,11+/m0/s1
InChIKeyMSPJPGIGNWYLAC-JVUFJMBOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@](CO)(O2)C#C
OpenEye OEToolkits 2.0.7C#C[C@]1([C@H](C[C@@H](O1)N2C=CC(=NC2=O)N)O)CO
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[C](CO)(O2)C#C
OpenEye OEToolkits 2.0.7C#CC1(C(CC(O1)N2C=CC(=NC2=O)N)O)CO
FormulaC11 H13 N3 O4
Name4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one
ChEMBLCHEMBL322215
DrugBank
ZINCZINC000003993852
PDB chain8ooj Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ooj 4'-Ethynyl-2'-Deoxycytidine (EdC) preferentially targets lymphoma and leukemia subtypes by inducing replicative stress
Resolution2.1 Å
Binding residue
(original residue number in PDB)
I30 E53 L82 F96 Q97 D133 F137 E196 E197
Binding residue
(residue number reindexed from 1)
I12 E35 L54 F68 Q69 D105 F109 E168 E169
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.1.113: deoxyguanosine kinase.
2.7.1.74: deoxycytidine kinase.
2.7.1.76: deoxyadenosine kinase.
Gene Ontology
Molecular Function
GO:0004136 deoxyadenosine kinase activity
GO:0004137 deoxycytidine kinase activity
GO:0004138 deoxyguanosine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0019136 deoxynucleoside kinase activity
GO:0042803 protein homodimerization activity
GO:0043771 cytidine kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006220 pyrimidine nucleotide metabolic process
GO:0009224 CMP biosynthetic process
GO:0016310 phosphorylation
GO:0106383 dAMP salvage
GO:1901135 carbohydrate derivative metabolic process
GO:1901293 nucleoside phosphate biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
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:8ooj, PDBe:8ooj, PDBj:8ooj
PDBsum8ooj
PubMed38064712
UniProtP27707|DCK_HUMAN Deoxycytidine kinase (Gene Name=DCK)

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