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PsychedeliaDokholyan Laboratory
TargetEnzymes

DNA polymerase beta

Named enzymes, including the metabolising cytochromes and the monoamine oxidases.

Measurements
3
Compounds
3
Binding constants
0
Median pX
—

I · Identity

What this target is

Its function as UniProt states it, where in a cell the protein is found, and which cell types and tissues transcribe its gene.

Protein

DPOLB_HUMANPOLBHomo sapiens

DNA polymerase beta

Repair polymerase that plays a key role in base-excision repair10556592,9207062,9572863. During this process, the damaged base is excised by specific DNA glycosylases, the DNA backbone is nicked at the abasic site by an apurinic/apyrimidic (AP) endonuclease, and POLB removes 5'-deoxyribose-phosphate from the preincised AP site acting as a 5'-deoxyribose-phosphate lyase (5'-dRP lyase); through its DNA polymerase activity, it adds one nucleotide to the 3' end of the arising single-nucleotide gap10556592,17526740,8841119,9556598,9572863,9614142. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases. It is also able to cleave sugar-phosphate bonds 3' to an intact AP site, acting as an AP lyase9614142

Quoted from UniProt’s FUNCTION annotation for P06746 (reviewed). The superscript numbers are UniProt’s own PubMed citations, kept in the sentence and in order, each linking to the paper it names.

What it acts with

STRING’s highest-confidence human functional partners. The combined score mixes several kinds of evidence, so each channel is shown separately — a partner supported by experiment is a different claim from one supported only by text mining, and for a receptor this is where its coupling appears as evidence rather than as assertion.

PartnerCombinedExperimentDatabaseText mining
XRCC10.9990.9110.5000.999
LIG30.9990.7080.5000.999
APEX10.9980.5100.9000.970
PARP10.9960.8040.5000.962
LIG10.9960.0960.9000.964
PNKP0.9950.7640.8000.903
PARP20.9950.6140.5000.976
FEN10.9870.0940.9000.857
TDP10.9630.8340.0000.786
NEIL10.9570.2360.7000.825

Where it sits in the cell

  • Vesicles
  • Cytosol

Human Protein Atlas, by antibody immunofluorescence in cell lines — a different assay from the expression figures below, which are RNA.

UniProt, curated Nucleus · Cytoplasm

Expression by cell type

Single cell type RNA, the 4 highest of those the Human Protein Atlas reports for this gene. Transcript, not protein, and a cell type rather than a tissue.

  • pDCs516.7 nCPM
  • Early spermatids315.8 nCPM
  • Late spermatids225.5 nCPM
  • Late primary spermatocytes137.5 nCPM

Expression by tissue

The tissues this gene is enriched in, by consensus RNA. A tissue absent from this list is one the Atlas does not call specific for this gene, which is not the same as absent from it.

  • brain176.1 nTPM

II · Anatomy

Where the gene is transcribed

The same two atlases the compound plates use, asked about this gene alone. Brain on the left, peripheral and autonomic tissues on the right.

Brain

cerebral cortex — 24.1 nTPM, from POLBcerebellum — 176.1 nTPM, from POLBhippocampal formation — 21.0 nTPM, from POLBamygdala — 25.0 nTPM, from POLBhypothalamus — 23.9 nTPM, from POLBthalamus — no resolved target expressed herebasal ganglia — 22.5 nTPM, from POLBmedulla oblongata — no resolved target expressed here

basal ganglia: drawn as the caudate nucleus, putamen and globus pallidus.

Measured but not drawn — this anatomogram has no outline for them: pituitary gland 26.0, spinal cord 23.2, midbrain 20.6, retina 16.7.

Body

heart — 24.7 nTPM, from POLBsmooth muscle — 9.9 nTPM, from POLBlung — 13.9 nTPM, from POLBliver — 31.7 nTPM, from POLBkidney — 17.5 nTPM, from POLBstomach — 13.2 nTPM, from POLBduodenum — 10.2 nTPM, from POLBsmall intestine — 10.4 nTPM, from POLBcolon — 11.5 nTPM, from POLBadrenal gland — 16.5 nTPM, from POLBthyroid gland — 13.3 nTPM, from POLBpancreas — 16.3 nTPM, from POLBurinary bladder — 28.8 nTPM, from POLBskeletal muscle — 80.0 nTPM, from POLBspleen — 16.7 nTPM, from POLBsalivary gland — 28.5 nTPM, from POLB
0176 nTPM

Square-root ramp · shared scale across both plates

Shading is transcript level — not affinity, and not affinity combined with expression. Outlined but unshaded organs hold none of POLB transcript above the atlas’s detection threshold. Anatomy from EMBL-EBI Anatomogram (Apache License 2.0); regions identified by Uberon (uberon.org), CC BY 3.0.

Brain · 10

  • cerebellum176.1 nTPM
  • pituitary gland26.0 nTPM
  • amygdala25.0 nTPM
  • cerebral cortex24.1 nTPM
  • hypothalamus23.9 nTPM
  • spinal cord23.2 nTPM
  • basal ganglia22.5 nTPM
  • hippocampal formation21.0 nTPM
  • midbrain20.6 nTPM
  • retina16.7 nTPM

Peripheral and autonomic · 16

  • skeletal muscle80.0 nTPM
  • liver31.7 nTPM
  • urinary bladder28.8 nTPM
  • salivary gland28.5 nTPM
  • heart muscle24.7 nTPM
  • kidney17.5 nTPM
  • spleen16.7 nTPM
  • adrenal gland16.5 nTPM
  • pancreas16.3 nTPM
  • lung13.9 nTPM
  • thyroid gland13.3 nTPM
  • stomach 113.2 nTPM
  • colon11.5 nTPM
  • small intestine10.4 nTPM
  • duodenum10.2 nTPM
  • smooth muscle9.9 nTPM

Transcript is not protein. These are RNA levels for POLB, shaded on √nTPM so that a three-order range stays legible — on a linear ramp every region but the strongest would read as blank, which looks like absence rather than less. A region carrying no shading is one the atlas reports no consensus value for, not one where the gene is silent. And a gene being transcribed somewhere is not evidence that any compound reaches it. Human Protein Atlas, RNA expression, nTPM (normalized transcripts per million), consensus tissue dataset.

IV · Evidence

Every measurement at this target

Each row links to the ChEMBL assay it came from.

Functional readouts 3

IC₅₀, EC₅₀, AC₅₀ and potency. Assay-dependent, and not interchangeable with a binding constant.

TargetClassTypeValue (nM)pXOrganismAssay
DNA polymerase betaEnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1614079
DNA polymerase betaEnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1614079
DNA polymerase betaEnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1614079
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