Details of the Target

General Information of Target

Target ID LDTP02870
Target Name Y-box-binding protein 3 (YBX3)
Gene Name YBX3
Gene ID 8531
Synonyms
CSDA; DBPA; Y-box-binding protein 3; Cold shock domain-containing protein A; DNA-binding protein A; Single-strand DNA-binding protein NF-GMB
3D Structure
Download
2D Sequence (FASTA)
Download
3D Structure (PDB)
Download
Sequence
MSEAGEATTTTTTTLPQAPTEAAAAAPQDPAPKSPVGSGAPQAAAPAPAAHVAGNPGGDA
APAATGTAAAASLATAAGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQ
TAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAADRRRYRRG
YYGRRRGPPRNYAGEEEEEGSGSSEGFDPPATDRQFSGARNQLRRPQYRPQYRQRRFPPY
HVGQTFDRRSRVLPHPNRIQAGEIGEMKDGVPEGAQLQGPVHRNPTYRPRYRSRGPPRPR
PAPAVGEAEDKENQQATSGPNQPSVRRGYRRPYNYRRRPRPPNAPSQDGKEAKAGEAPTE
NPAPPTQQSSAE
Target Bioclass
Transcription factor
Subcellular location
Cytoplasm
Function
Binds to the GM-CSF promoter. Seems to act as a repressor. Binds also to full-length mRNA and to short RNA sequences containing the consensus site 5'-UCCAUCA-3'. May have a role in translation repression.
Uniprot ID
P16989
Ensemble ID
ENST00000228251.9
HGNC ID
HGNC:2428
ChEMBL ID
CHEMBL4295720

Target Site Mutations in Different Cell Lines

Cell line Mutation details Probe for labeling this protein in this cell
HCC44 SNV: p.A63T .
HT SNV: p.Y192C .
P31FUJ SNV: p.A43D .
WM2664 Insertion: p.R169LfsTer37 .

Probe(s) Labeling This Target

ABPP Probe
Click To Hide/Show 10 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
C-Sul
 Probe Info  		68.24  LDD0066  [1]
TH211
 Probe Info  		Y104(6.69)  LDD0257  [2]
Acrolein
 Probe Info  		H282(0.00); H51(0.00)  LDD0223  [3]
5E-2FA
 Probe Info  		H282(0.00); H119(0.00)  LDD2235  [4]
ATP probe
 Probe Info  		K124(0.00); K125(0.00); K268(0.00); K311(0.00)  LDD0199  [5]
m-APA
 Probe Info  		H282(0.00); H119(0.00); H241(0.00)  LDD2231  [4]
1d-yne
 Probe Info  		N.A.  LDD0358  [6]
ATP probe
 Probe Info  		N.A.  LDD0035  [7]
SF
 Probe Info  		K113(0.00); K125(0.00); K124(0.00)  LDD0028  [8]
1c-yne
 Probe Info  		K311(0.00); K268(0.00)  LDD0228  [6]
PAL-AfBPP Probe
Click To Hide/Show 8 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
C346
 Probe Info  		11.24  LDD2007  [9]
C347
 Probe Info  		5.21  LDD2008  [9]
C364
 Probe Info  		20.39  LDD2025  [9]
FFF probe13
 Probe Info  		20.00  LDD0475  [10]
FFF probe2
 Probe Info  		17.89  LDD0463  [10]
FFF probe3
 Probe Info  		18.27  LDD0464  [10]
FFF probe4
 Probe Info  		20.00  LDD0466  [10]
FFF probe6
 Probe Info  		5.79  LDD0468  [10]

Competitor(s) Related to This Target

Competitor ID Name Cell line Binding Site(Ratio) Interaction ID Ref
 LDCM0191  Compound 21 HEK-293T 8.96  LDD0508  [10]
 LDCM0190  Compound 34 HEK-293T 10.32  LDD0510  [10]
 LDCM0192  Compound 35 HEK-293T 5.55  LDD0509  [10]
 LDCM0193  Compound 36 HEK-293T 16.61  LDD0511  [10]
 LDCM0109  NEM HeLa H282(0.00); H51(0.00)  LDD0223  [3]

The Interaction Atlas With This Target

The Protein(s) Related To This Target

Enzyme
Click To Hide/Show 1 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (PPP1CA) PPP phosphatase family P62136

References

1 Low-Toxicity Sulfonium-Based Probes for Cysteine-Specific Profiling in Live Cells. Anal Chem. 2022 Mar 15;94(10):4366-4372. doi: 10.1021/acs.analchem.1c05129. Epub 2022 Mar 4.
2 Chemoproteomic profiling of kinases in live cells using electrophilic sulfonyl triazole probes. Chem Sci. 2021 Jan 21;12(9):3295-3307. doi: 10.1039/d0sc06623k.
3 ACR-Based Probe for the Quantitative Profiling of Histidine Reactivity in the Human Proteome. J Am Chem Soc. 2023 Mar 8;145(9):5252-5260. doi: 10.1021/jacs.2c12653. Epub 2023 Feb 27.
4 Global profiling of functional histidines in live cells using small-molecule photosensitizer and chemical probe relay labelling. Nat Chem. 2024 Jun 4. doi: 10.1038/s41557-024-01545-6. Online ahead of print.
Mass spectrometry data entry: PXD042377
5 Targeted Proteomic Approaches for Proteome-Wide Characterizations of the AMP-Binding Capacities of Kinases. J Proteome Res. 2022 Aug 5;21(8):2063-2070. doi: 10.1021/acs.jproteome.2c00225. Epub 2022 Jul 12.
6 Tunable Amine-Reactive Electrophiles for Selective Profiling of Lysine. Angew Chem Int Ed Engl. 2022 Jan 26;61(5):e202112107. doi: 10.1002/anie.202112107. Epub 2021 Dec 16.
7 Comparison of Quantitative Mass Spectrometry Platforms for Monitoring Kinase ATP Probe Uptake in Lung Cancer. J Proteome Res. 2018 Jan 5;17(1):63-75. doi: 10.1021/acs.jproteome.7b00329. Epub 2017 Nov 22.
Mass spectrometry data entry: PXD006095 , PXD006096
8 Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows. bioRxiv [Preprint]. 2023 Feb 18:2023.02.17.529022. doi: 10.1101/2023.02.17.529022.
Mass spectrometry data entry: PXD039931
9 Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells. Science. 2024 Apr 26;384(6694):eadk5864. doi: 10.1126/science.adk5864. Epub 2024 Apr 26.
Mass spectrometry data entry: PXD041587
10 Ligand and Target Discovery by Fragment-Based Screening in Human Cells. Cell. 2017 Jan 26;168(3):527-541.e29. doi: 10.1016/j.cell.2016.12.029. Epub 2017 Jan 19.