Structure of PDB 2zi3 Chain A Binding Site BS02

Receptor Information
>2zi3 Chain A (length=241) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNVQSTQDEFE
ELTMSQKNGGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDA
EKPVLFFERSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQS
LELDGIIYLQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHR
TLKTNFDYLQEVPILTLDVNEDFKDKYASLVEKVKEFLSTL
Ligand information
Ligand ID3D1
InChIInChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m0/s1
InChIKeyOLXZPDWKRNYJJZ-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)CO)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO)O3
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3)CO)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO)O)N
FormulaC10 H13 N5 O3
Name(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol;
2'-DEOXYADENOSINE
ChEMBLCHEMBL449329
DrugBank
ZINCZINC000001081581
PDB chain2zi3 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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PDB2zi3 Structural basis for substrate promiscuity of dCK
Resolution2.3 Å
Binding residue
(original residue number in PDB)
I30 E53 W58 L82 Y86 F96 Q97 D133 F137 E197
Binding residue
(residue number reindexed from 1)
I11 E34 W39 L63 Y67 F77 Q78 D114 F118 E178
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E53 R128
Catalytic site (residue number reindexed from 1) E34 R109
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:2zi3, PDBe:2zi3, PDBj:2zi3
PDBsum2zi3
PubMed18377927
UniProtP27707|DCK_HUMAN Deoxycytidine kinase (Gene Name=DCK)

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