Structure of PDB 3ipy Chain A Binding Site BS01

Receptor Information
>3ipy Chain A (length=225) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIKKISIEGNIAAGKSTFVNILKQLCEDWEVVPEPVARWCNNGGNVLQMM
YEKPERWSFTFQTYACLSRIRAQLASLNGKLKDAEKPVLFFERSVYSDRY
IFASNLYESECMNETEWTIYQDWHDWMNNQFGQSLELDGIIYLQATPETC
LHRIYLRGRNEEQGIPLEYLEKLHYKHESWLLHRTLKTNFDYLQEVPILT
LDVNEDFKDKYESLVEKVKEFLSTL
Ligand information
Ligand IDB87
InChIInChI=1S/C22H25N5OS/c28-22(27-7-3-4-8-27)15-25-9-11-26(12-10-25)21-14-18(23-16-24-21)20-13-17-5-1-2-6-19(17)29-20/h1-2,5-6,13-14,16H,3-4,7-12,15H2
InChIKeyNDLZMZLRTHDNSQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02O=C(N1CCCC1)CN5CCN(c4ncnc(c3sc2ccccc2c3)c4)CC5
CACTVS 3.352O=C(CN1CCN(CC1)c2cc(ncn2)c3sc4ccccc4c3)N5CCCC5
OpenEye OEToolkits 1.7.0c1ccc2c(c1)cc(s2)c3cc(ncn3)N4CCN(CC4)CC(=O)N5CCCC5
FormulaC22 H25 N5 O S
Name4-(1-benzothiophen-2-yl)-6-[4-(2-oxo-2-pyrrolidin-1-ylethyl)piperazin-1-yl]pyrimidine
ChEMBLCHEMBL1081559
DrugBank
ZINCZINC000096315970
PDB chain3ipy Chain A Residue 263 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ipy Lead optimization and structure-based design of potent and bioavailable deoxycytidine kinase inhibitors.
Resolution2.54 Å
Binding residue
(original residue number in PDB)		I30 E53 F96 D133 F137 I200 P201 Y204
Binding residue
(residue number reindexed from 1)		I11 E34 F61 D98 F102 I165 P166 Y169
Annotation score1
Binding affinityBindingDB: IC50=510nM
Enzymatic activity
Catalytic site (original residue number in PDB) E53 R128
Catalytic site (residue number reindexed from 1) E34 R93
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:3ipy, PDBe:3ipy, PDBj:3ipy
PDBsum3ipy
PubMed19836232
UniProtP27707|DCK_HUMAN Deoxycytidine kinase (Gene Name=DCK)

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