Structure of PDB 4jlm Chain A Binding Site BS01

Receptor Information
>4jlm Chain A (length=233) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRIKKISIEGNIAAGKSTFVNILKQLSEDWEVVPEPVARWSNELTMEQKN
GGNVLQMMYEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFE
RSVYSDRYIFASNLYESESMNETEWTIYQDWHDWMNNQFGQSLELDGIIY
LQATPETCLHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDY
LQEVPILTLDVNEDFKDKYESLVEKVKEFLSTL
Ligand information
Ligand ID1NN
InChIInChI=1S/C19H22FN5O2S2/c1-3-15-12(10-28-19-24-16(21)9-17(22)25-19)23-18(29-15)11-4-5-13(26-2)14(8-11)27-7-6-20/h4-5,8-9H,3,6-7,10H2,1-2H3,(H4,21,22,24,25)
InChIKeyBLYJASYJWHXVPZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FCCOc1c(OC)ccc(c1)c2nc(c(s2)CC)CSc3nc(N)cc(n3)N
CACTVS 3.370CCc1sc(nc1CSc2nc(N)cc(N)n2)c3ccc(OC)c(OCCF)c3
OpenEye OEToolkits 1.7.6CCc1c(nc(s1)c2ccc(c(c2)OCCF)OC)CSc3nc(cc(n3)N)N
FormulaC19 H22 F N5 O2 S2
Name2-[({5-ethyl-2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine
ChEMBLCHEMBL2426598
DrugBank
ZINCZINC000095921200
PDB chain4jlm 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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PDB4jlm Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules.
Resolution2.18 Å
Binding residue
(original residue number in PDB)		E53 V55 M85 Y86 P89 Q97 D133 F137 S144 Y204
Binding residue
(residue number reindexed from 1)		E35 V37 M58 Y59 P62 Q70 D106 F110 S117 Y177
Annotation score1
Binding affinityMOAD: Ki=6.1nM
PDBbind-CN: -logKd/Ki=7.64,IC50=22.7nM
BindingDB: IC50=7.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) E53 R128
Catalytic site (residue number reindexed from 1) E35 R101
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:4jlm, PDBe:4jlm, PDBj:4jlm
PDBsum4jlm
PubMed24419380
UniProtP27707|DCK_HUMAN Deoxycytidine kinase (Gene Name=DCK)

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