Structure of PDB 4q1d Chain B

Receptor sequence
>4q1dB (length=227) Species: 9606 (Homo sapiens) [Search protein sequence]
RIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNLTMEQKNGG
NVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERS
VYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQLELDGIIYLQATPE
TCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPI
LTLDVNEDFKDKYESLVEKVKEFLSTL
3D structure
PDB4q1d Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability.
ChainB
Resolution2.0 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) E53 R128
Catalytic site (residue number reindexed from 1) E34 R99
Enzyme Commision number 2.7.1.113: deoxyguanosine kinase.
2.7.1.74: deoxycytidine kinase.
2.7.1.76: deoxyadenosine kinase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 2Y1 B E53 V55 Y86 P89 F96 Q97 D133 F137 S144 Y204 E34 V36 Y57 P60 F67 Q68 D104 F108 S115 Y171 MOAD: Ki=16.6nM
BindingDB: IC50=10.0nM,Ki=17nM
BS02 UDP B A31 A32 G33 K34 S35 T36 R188 R192 D241 F242 K243 A12 A13 G14 K15 S16 T17 R155 R159 D208 F209 K210
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:4q1d, PDBe:4q1d, PDBj:4q1d
PDBsum4q1d
PubMed25341194
UniProtP27707|DCK_HUMAN Deoxycytidine kinase (Gene Name=DCK)

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