Structure of PDB 4q1d Chain A Binding Site BS01

Receptor Information
>4q1d Chain A (length=231) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNLTMEQKNGG
NVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERS
VYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQ
ATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQ
EVPILTLDVNEDFKDKYESLVEKVKEFLSTL
Ligand information
Ligand ID2Y1
InChIInChI=1S/C21H26FN5O2S2/c1-4-5-16-19(12(2)30-21-25-17(23)11-18(24)26-21)27-20(31-16)13-6-7-14(28-3)15(10-13)29-9-8-22/h6-7,10-12H,4-5,8-9H2,1-3H3,(H4,23,24,25,26)/t12-/m1/s1
InChIKeyMGRJEGAUWXSZGM-GFCCVEGCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCc1sc(nc1[C@@H](C)Sc2nc(N)cc(N)n2)c3ccc(OC)c(OCCF)c3
CACTVS 3.385CCCc1sc(nc1[CH](C)Sc2nc(N)cc(N)n2)c3ccc(OC)c(OCCF)c3
OpenEye OEToolkits 1.7.6CCCc1c(nc(s1)c2ccc(c(c2)OCCF)OC)C(C)Sc3nc(cc(n3)N)N
ACDLabs 12.01FCCOc1c(OC)ccc(c1)c2nc(c(s2)CCC)C(Sc3nc(N)cc(n3)N)C
OpenEye OEToolkits 1.7.6CCCc1c(nc(s1)c2ccc(c(c2)OCCF)OC)[C@@H](C)Sc3nc(cc(n3)N)N
FormulaC21 H26 F N5 O2 S2
Name(R)-2-((1-(2-(3-(2-fluoroethoxy)-4-methoxyphenyl)-5-propylthiazol-4-yl)ethyl)thio)pyrimidine-4,6-diamine;
2-{[(1R)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-propyl-1,3-thiazol-4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine
ChEMBL
DrugBank
ZINCZINC000223775728
PDB chain4q1d 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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PDB4q1d Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		E53 V55 L82 Y86 P89 Q97 D133 F137 L141 S144 Y204
Binding residue
(residue number reindexed from 1)		E34 V36 L53 Y57 P60 Q68 D104 F108 L112 S115 Y175
Annotation score1
Binding affinityMOAD: Ki=16.6nM
PDBbind-CN: -logKd/Ki=7.78,Ki=16.6nM
BindingDB: IC50=10.0nM,Ki=17nM
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.
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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