Structure of PDB 2no0 Chain B Binding Site BS02

Receptor Information
>2no0 Chain B (length=225) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNVQSTNGGNV
LQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLDAEKPVLFFERSVYS
DRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATP
ETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVP
ILTLDVNEDFYESLVEKVKEFLSTL
Ligand information
Ligand IDGEO
InChIInChI=1S/C9H11F2N3O4/c10-9(11)6(16)4(3-15)18-7(9)14-2-1-5(12)13-8(14)17/h1-2,4,6-7,15-16H,3H2,(H2,12,13,17)/t4-,6-,7-/m1/s1
InChIKeySDUQYLNIPVEERB-QPPQHZFASA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)C2(F)F
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)C2(F)F
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)(F)F
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)CO)O)(F)F
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2(F)F)CO
FormulaC9 H11 F2 N3 O4
NameGEMCITABINE;
2',2'-DIFLUORODEOXYCYTIDINE
ChEMBLCHEMBL888
DrugBankDB00441
ZINCZINC000018279854
PDB chain2no0 Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2no0 Nonenantioselectivity Property of Human Deoxycytidine Kinase Explained by Structures of the Enzyme in Complex with l- and d-Nucleosides.
Resolution1.8 Å
Binding residue
(original residue number in PDB)
I30 E53 Y86 F96 Q97 R128 D133 F137 E197
Binding residue
(residue number reindexed from 1)
I11 E34 Y55 F65 Q66 R96 D101 F105 E165
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) E53 R128
Catalytic site (residue number reindexed from 1) E34 R96
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:2no0, PDBe:2no0, PDBj:2no0
PDBsum2no0
PubMed17530837
UniProtP27707|DCK_HUMAN Deoxycytidine kinase (Gene Name=DCK)

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