Structure of PDB 4q1a Chain A Binding Site BS01

Receptor Information
>4q1a Chain A (length=230) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSLTMEQKNGGN
VLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSV
YSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQA
TPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQE
VPILTLDVNEDFKDKYESLVEKVKEFLSTL
Ligand information
Ligand ID2XZ
InChIInChI=1S/C20H25N5O3S2/c1-3-4-16-13(11-29-20-24-17(21)10-18(22)25-20)23-19(30-16)12-5-6-14(27-2)15(9-12)28-8-7-26/h5-6,9-10,26H,3-4,7-8,11H2,1-2H3,(H4,21,22,24,25)
InChIKeyIFMIBDOPTYIDDA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCc1c(nc(s1)c2ccc(c(c2)OCCO)OC)CSc3nc(cc(n3)N)N
CACTVS 3.385CCCc1sc(nc1CSc2nc(N)cc(N)n2)c3ccc(OC)c(OCCO)c3
ACDLabs 12.01n1c(c(sc1c2cc(OCCO)c(OC)cc2)CCC)CSc3nc(N)cc(n3)N
FormulaC20 H25 N5 O3 S2
Name2-(5-(4-(((4,6-diaminopyrimidin-2-yl)thio)methyl)-5-propylthiazol-2-yl)-2-methoxyphenoxy)ethan-1-ol;
2-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethanol
ChEMBLCHEMBL2426570
DrugBank
ZINCZINC000096283896
PDB chain4q1a Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4q1a Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		E53 V55 L82 Y86 P89 F96 Q97 D133 F137 S146 Y204
Binding residue
(residue number reindexed from 1)		E34 V36 L52 Y56 P59 F66 Q67 D103 F107 S116 Y174
Annotation score1
Binding affinityMOAD: Ki=0.5nM
PDBbind-CN: -logKd/Ki=9.30,Ki=0.5nM
BindingDB: IC50=1.2nM,Ki=0.500000nM
Enzymatic activity
Catalytic site (original residue number in PDB) E53 R128
Catalytic site (residue number reindexed from 1) E34 R98
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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Biological Process
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Cellular Component
External links
PDB RCSB:4q1a, PDBe:4q1a, PDBj:4q1a
PDBsum4q1a
PubMed25341194
UniProtP27707|DCK_HUMAN Deoxycytidine kinase (Gene Name=DCK)

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