Structure of PDB 4q18 Chain B Binding Site BS03

Receptor Information
>4q18 Chain B (length=231) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSLTMEQKNGG
NVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERS
VYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQ
ATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQ
EVPILTLDVNEDFKDKYESLVEKVKEFLSTL
Ligand information
Ligand ID2XJ
InChIInChI=1S/C22H29N5O3S2/c1-5-6-17-14(11-31-19-10-18(23)26-21(24)27-19)25-20(32-17)13-7-8-15(29-4)16(9-13)30-12-22(2,3)28/h7-10,28H,5-6,11-12H2,1-4H3,(H4,23,24,26,27)
InChIKeyVSEGZQPURWAQMY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01n1c(c(sc1c2cc(OCC(O)(C)C)c(OC)cc2)CCC)CSc3nc(nc(N)c3)N
OpenEye OEToolkits 1.7.6CCCc1c(nc(s1)c2ccc(c(c2)OCC(C)(C)O)OC)CSc3cc(nc(n3)N)N
CACTVS 3.385CCCc1sc(nc1CSc2cc(N)nc(N)n2)c3ccc(OC)c(OCC(C)(C)O)c3
FormulaC22 H29 N5 O3 S2
Name1-(5-(4-(((2,6-diaminopyrimidin-4-yl)thio)methyl)-5-propylthiazol-2-yl)-2-methoxyphenoxy)-2-methylpropan-2-ol;
1-[5-(4-{[(2,6-diaminopyrimidin-4-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]-2-methylpropan-2-ol
ChEMBLCHEMBL3358092
DrugBank
ZINCZINC000224698309
PDB chain4q18 Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4q18 Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		S59 Y86 R194 E196 E197 G199 I200 P201 Y204
Binding residue
(residue number reindexed from 1)		S41 Y57 R165 E167 E168 G170 I171 P172 Y175
Annotation score1
Binding affinityMOAD: Ki=735nM
BindingDB: IC50=754nM,Ki=735nM
Enzymatic activity
Catalytic site (original residue number in PDB) E53 R128
Catalytic site (residue number reindexed from 1) E35 R99
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:4q18, PDBe:4q18, PDBj:4q18
PDBsum4q18
PubMed25341194
UniProtP27707|DCK_HUMAN Deoxycytidine kinase (Gene Name=DCK)

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