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PsychedeliaDokholyan Laboratory
TargetEnzymes

Tyrosyl-DNA phosphodiesterase 1

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

Measurements
68
Compounds
25
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

TYDP1_HUMANTDP1Homo sapiens

Tyrosyl-DNA phosphodiesterase 1

DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3'-phosphoglycolates on protruding 3' ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3'exonuclease activity and can remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate

Quoted from UniProt’s FUNCTION annotation for Q9NUW8 (reviewed).

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
LIG30.9920.8050.0000.954
TOP10.9920.6460.0000.978
XRCC10.9890.6880.0000.963
APTX0.9640.5910.0000.912
POLB0.9630.8340.0000.786
PNKP0.9290.1450.0000.919
TDP20.9180.0000.0000.912
PARP10.9090.1980.0000.889
APLF0.9050.7800.0000.589
APEX10.9040.2890.0000.860

Where it sits in the cell

  • Nucleoplasm
  • Plasma membraneadditional

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

  • Early spermatids165.8 nCPM
  • Late primary spermatocytes100.2 nCPM
  • Oocytes78.3 nCPM

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 — 5.2 nTPM, from TDP1cerebellum — 5.6 nTPM, from TDP1hippocampal formation — 3.2 nTPM, from TDP1amygdala — 3.2 nTPM, from TDP1hypothalamus — 3.8 nTPM, from TDP1thalamus — no resolved target expressed herebasal ganglia — 3.5 nTPM, from TDP1medulla 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: retina 4.6, pituitary gland 4.3, midbrain 3.8, spinal cord 3.4.

Body

heart — 2.4 nTPM, from TDP1smooth muscle — 5.8 nTPM, from TDP1lung — 4.4 nTPM, from TDP1liver — 6.0 nTPM, from TDP1kidney — 6.5 nTPM, from TDP1stomach — 7.5 nTPM, from TDP1duodenum — 6.1 nTPM, from TDP1small intestine — 6.5 nTPM, from TDP1colon — 7.4 nTPM, from TDP1adrenal gland — 3.7 nTPM, from TDP1thyroid gland — 4.6 nTPM, from TDP1pancreas — 4.5 nTPM, from TDP1urinary bladder — 7.6 nTPM, from TDP1skeletal muscle — 2.0 nTPM, from TDP1spleen — 10.0 nTPM, from TDP1salivary gland — 5.2 nTPM, from TDP1
010 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 TDP1 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

  • cerebellum5.6 nTPM
  • cerebral cortex5.2 nTPM
  • retina4.6 nTPM
  • pituitary gland4.3 nTPM
  • hypothalamus3.8 nTPM
  • midbrain3.8 nTPM
  • basal ganglia3.5 nTPM
  • spinal cord3.4 nTPM
  • hippocampal formation3.2 nTPM
  • amygdala3.2 nTPM

Peripheral and autonomic · 16

  • spleen10.0 nTPM
  • urinary bladder7.6 nTPM
  • stomach 17.5 nTPM
  • colon7.4 nTPM
  • kidney6.5 nTPM
  • small intestine6.5 nTPM
  • duodenum6.1 nTPM
  • liver6.0 nTPM
  • smooth muscle5.8 nTPM
  • salivary gland5.2 nTPM
  • thyroid gland4.6 nTPM
  • pancreas4.5 nTPM
  • lung4.4 nTPM
  • adrenal gland3.7 nTPM
  • heart muscle2.4 nTPM
  • skeletal muscle2.0 nTPM

Transcript is not protein. These are RNA levels for TDP1, 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 68

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

TargetClassTypeValue (nM)pXOrganismAssay
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354221
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL2354254
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1614364
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1614364
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1614364
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1614364
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1614364
Tyrosyl-DNA phosphodiesterase 1EnzymesPotency— no normalized value— value does not convert to pXHomo sapiensCHEMBL1614364
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