Structure of PDB 3lk9 Chain A Binding Site BS04

Receptor Information
>3lk9 Chain A (length=326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEA
KKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPS
AARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQ
DIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRL
IPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGE
PLPVDSEKDIFDYIQWKYREPKDRSE
Ligand information
Ligand IDTFF
InChIInChI=1S/C12H17F4N2O12P3/c1-5-3-18(10(21)17-9(5)20)8-2-6(19)7(30-8)4-29-33(27,28)12(15,16)31(22,23)11(13,14)32(24,25)26/h3,6-8,19H,2,4H2,1H3,(H,22,23)(H,27,28)(H,17,20,21)(H2,24,25,26)/t6-,7+,8+/m0/s1
InChIKeyHHJYLFURQLSDJT-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)C(F)(F)[P](O)(=O)C(F)(F)[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 1.7.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(C(F)(F)P(=O)(C(F)(F)P(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(C(F)(F)[P@@](=O)(C(F)(F)P(=O)(O)O)O)O)O
CACTVS 3.352CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)C(F)(F)[P](O)(=O)C(F)(F)[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC12 H17 F4 N2 O12 P3
Name5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl](difluoro)methyl}(hydroxy)phosphoryl]thymidine
ChEMBL
DrugBank
ZINCZINC000058655529
PDB chain3lk9 Chain A Residue 338 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3lk9 Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		S180 R183 S188 G189 D190 D192 Y271 F272 T273 G274 D276 N279
Binding residue
(residue number reindexed from 1)		S171 R174 S179 G180 D181 D183 Y262 F263 T264 G265 D267 N270
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D190 D192 D256
Catalytic site (residue number reindexed from 1) D181 D183 D247
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
4.2.99.-
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0016779 nucleotidyltransferase activity
GO:0016829 lyase activity
GO:0019899 enzyme binding
GO:0034061 DNA polymerase activity
GO:0046872 metal ion binding
GO:0051575 5'-deoxyribose-5-phosphate lyase activity
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological Process
GO:0001701 in utero embryonic development
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006287 base-excision repair, gap-filling
GO:0006290 pyrimidine dimer repair
GO:0006297 nucleotide-excision repair, DNA gap filling
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006915 apoptotic process
GO:0006954 inflammatory response
GO:0006974 DNA damage response
GO:0007435 salivary gland morphogenesis
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010332 response to gamma radiation
GO:0016445 somatic diversification of immunoglobulins
GO:0016446 somatic hypermutation of immunoglobulin genes
GO:0045471 response to ethanol
GO:0048535 lymph node development
GO:0048536 spleen development
GO:0048872 homeostasis of number of cells
GO:0051402 neuron apoptotic process
GO:0055093 response to hyperoxia
GO:0071707 immunoglobulin heavy chain V-D-J recombination
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005874 microtubule
GO:0005876 spindle microtubule
GO:0032991 protein-containing complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3lk9, PDBe:3lk9, PDBj:3lk9
PDBsum3lk9
PubMed20724659
UniProtP06746|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

[Back to BioLiP]