Structure of PDB 4q1d Chain A

Receptor sequence
>4q1dA (length=231) Species: 9606 (Homo sapiens) [Search protein sequence]
RIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNLTMEQKNGG
NVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERS
VYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQ
ATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQ
EVPILTLDVNEDFKDKYESLVEKVKEFLSTL
3D structure
PDB4q1d Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability.
ChainA
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 A E53 V55 L82 Y86 P89 Q97 D133 F137 L141 S144 Y204 E34 V36 L53 Y57 P60 Q68 D104 F108 L112 S115 Y175 MOAD: Ki=16.6nM
PDBbind-CN: -logKd/Ki=7.78,Ki=16.6nM
BindingDB: IC50=10.0nM,Ki=17nM
BS02 UDP A A31 G33 K34 S35 T36 R188 R192 D241 F242 A12 G14 K15 S16 T17 R159 R163 D212 F213
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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