General Information of Target

Target ID LDTP05065
Target Name Y-box-binding protein 1 (YBX1)
Gene Name YBX1
Gene ID 4904
Synonyms
NSEP1; YB1; Y-box-binding protein 1; YB-1; CCAAT-binding transcription factor I subunit A; CBF-A; DNA-binding protein B; DBPB; Enhancer factor I subunit A; EFI-A; Nuclease-sensitive element-binding protein 1; Y-box transcription factor
3D Structure
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2D Sequence (FASTA)
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3D Structure (PDB)
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Sequence
MSSEAETQQPPAAPPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPAGGDKKVIATKVL
GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGA
EAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEG
QAQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRG
YRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDG
KETKAADPPAENSSAPEAEQGGAE
Target Bioclass
Transcription factor
Family
YBX1 family
Subcellular location
Cytoplasm
Function
DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation . Predominantly acts as a RNA-binding protein: binds preferentially to the 5'-[CU]CUGCG-3' RNA motif and specifically recognizes mRNA transcripts modified by C5-methylcytosine (m5C). Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay. Component of the CRD-mediated complex that promotes MYC mRNA stability. Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors. Plays a key role in RNA composition of extracellular exosomes by defining the sorting of small non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs. Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs. Acts as a key effector of epidermal progenitors by preventing epidermal progenitor senescence: acts by regulating the translation of a senescence-associated subset of cytokine mRNAs, possibly by binding to m5C-containing mRNAs. Also involved in pre-mRNA alternative splicing regulation: binds to splice sites in pre-mRNA and regulates splice site selection. Binds to TSC22D1 transcripts, thereby inhibiting their translation and negatively regulating TGF-beta-mediated transcription of COL1A2. Also able to bind DNA: regulates transcription of the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes. Promotes separation of DNA strands that contain mismatches or are modified by cisplatin. Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair. The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.
Uniprot ID
P67809
Ensemble ID
ENST00000321358.12
HGNC ID
HGNC:8014
ChEMBL ID
CHEMBL4296006

Probe(s) Labeling This Target

ABPP Probe
Click To Hide/Show 19 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
A-EBA
 Probe Info 
3.84  LDD0215  [1]
AZ-9
 Probe Info 
2.05  LDD0393  [2]
TH211
 Probe Info 
Y158(20.00); Y162(20.00); Y208(20.00); Y138(15.62)  LDD0257  [3]
TH216
 Probe Info 
Y138(8.11)  LDD0259  [3]
OPA-S-S-alkyne
 Probe Info 
K264(4.18); K137(7.50); K170(9.44)  LDD3494  [4]
Probe 1
 Probe Info 
Y138(43.21); Y145(12.46); Y162(1,081.18); Y208(202.56)  LDD3495  [5]
HHS-482
 Probe Info 
Y158(1.12); Y162(0.88); Y72(1.06)  LDD0285  [6]
HHS-475
 Probe Info 
Y208(0.70); Y158(0.78); Y162(1.10)  LDD0264  [7]
Acrolein
 Probe Info 
N.A.  LDD0221  [8]
AMP probe
 Probe Info 
N.A.  LDD0200  [9]
ATP probe
 Probe Info 
K137(0.00); K170(0.00); K304(0.00)  LDD0199  [9]
1d-yne
 Probe Info 
N.A.  LDD0356  [10]
NHS
 Probe Info 
K81(0.00); K137(0.00); K64(0.00)  LDD0010  [11]
SF
 Probe Info 
K81(0.00); Y208(0.00); Y162(0.00); K93(0.00)  LDD0028  [12]
STPyne
 Probe Info 
N.A.  LDD0009  [11]
Ox-W18
 Probe Info 
N.A.  LDD2175  [13]
1c-yne
 Probe Info 
K264(0.00); K170(0.00); K92(0.00); K137(0.00)  LDD0228  [10]
Methacrolein
 Probe Info 
N.A.  LDD0218  [8]
HHS-465
 Probe Info 
Y158(0.00); Y162(0.00); Y208(0.00); K170(0.00)  LDD2240  [14]
PAL-AfBPP Probe
Click To Hide/Show 34 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
C040
 Probe Info 
8.75  LDD1740  [15]
C041
 Probe Info 
6.54  LDD1741  [15]
C082
 Probe Info 
4.99  LDD1774  [15]
C085
 Probe Info 
4.92  LDD1777  [15]
C087
 Probe Info 
18.77  LDD1779  [15]
C131
 Probe Info 
6.11  LDD1813  [15]
C165
 Probe Info 
15.56  LDD1845  [15]
C170
 Probe Info 
8.82  LDD1850  [15]
C210
 Probe Info 
49.87  LDD1884  [15]
C211
 Probe Info 
8.22  LDD1885  [15]
C212
 Probe Info 
6.68  LDD1886  [15]
C213
 Probe Info 
15.45  LDD1887  [15]
C214
 Probe Info 
6.54  LDD1888  [15]
C232
 Probe Info 
36.25  LDD1905  [15]
C249
 Probe Info 
12.64  LDD1922  [15]
C280
 Probe Info 
9.58  LDD1950  [15]
C284
 Probe Info 
20.97  LDD1954  [15]
C313
 Probe Info 
18.90  LDD1980  [15]
C314
 Probe Info 
13.18  LDD1981  [15]
C338
 Probe Info 
12.13  LDD2001  [15]
C347
 Probe Info 
5.10  LDD2008  [15]
C353
 Probe Info 
6.68  LDD2014  [15]
C354
 Probe Info 
7.73  LDD2015  [15]
C364
 Probe Info 
18.00  LDD2025  [15]
C391
 Probe Info 
16.68  LDD2050  [15]
FFF probe11
 Probe Info 
12.13  LDD0471  [16]
FFF probe13
 Probe Info 
20.00  LDD0475  [16]
FFF probe2
 Probe Info 
18.36  LDD0463  [16]
FFF probe3
 Probe Info 
18.70  LDD0464  [16]
FFF probe6
 Probe Info 
9.43  LDD0467  [16]
FFF probe9
 Probe Info 
11.93  LDD0470  [16]
JN0003
 Probe Info 
20.00  LDD0469  [16]
DA-2
 Probe Info 
N.A.  LDD0070  [17]
STS-1
 Probe Info 
N.A.  LDD0068  [18]

Competitor(s) Related to This Target

Competitor ID Name Cell line Binding Site(Ratio) Interaction ID Ref
 LDCM0108  Chloroacetamide HeLa N.A.  LDD0222  [8]
 LDCM0116  HHS-0101 DM93 Y208(0.70); Y158(0.78); Y162(1.10)  LDD0264  [7]
 LDCM0117  HHS-0201 DM93 Y158(0.76); Y162(0.86); Y208(1.34)  LDD0265  [7]
 LDCM0118  HHS-0301 DM93 Y208(0.73); Y158(0.87); Y162(0.93)  LDD0266  [7]
 LDCM0119  HHS-0401 DM93 Y208(0.81); Y158(0.85); Y162(1.13)  LDD0267  [7]
 LDCM0120  HHS-0701 DM93 Y158(0.80); Y208(0.97); Y162(1.05)  LDD0268  [7]
 LDCM0107  IAA HeLa N.A.  LDD0221  [8]
 LDCM0123  JWB131 DM93 Y158(1.12); Y162(0.88); Y72(1.06)  LDD0285  [6]
 LDCM0124  JWB142 DM93 Y158(1.58); Y162(1.58); Y72(1.00)  LDD0286  [6]
 LDCM0125  JWB146 DM93 Y158(1.56); Y162(1.87); Y72(0.88)  LDD0287  [6]
 LDCM0126  JWB150 DM93 Y158(8.25); Y162(4.74); Y72(2.57)  LDD0288  [6]
 LDCM0127  JWB152 DM93 Y158(2.74); Y162(3.19); Y72(1.59)  LDD0289  [6]
 LDCM0128  JWB198 DM93 Y158(0.80); Y162(1.27); Y72(1.83)  LDD0290  [6]
 LDCM0129  JWB202 DM93 Y158(0.89); Y162(1.11); Y72(1.46)  LDD0291  [6]
 LDCM0130  JWB211 DM93 Y158(1.67); Y162(1.51); Y72(1.11)  LDD0292  [6]
 LDCM0109  NEM HeLa N.A.  LDD0223  [8]

The Interaction Atlas With This Target

The Protein(s) Related To This Target

Enzyme
Click To Hide/Show 4 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Cullin-1 (CUL1) Cullin family Q13616
ATP-dependent RNA helicase A (DHX9) DEAD box helicase family Q08211
Protein phosphatase 1G (PPM1G) PP2C family O15355
Histone acetyltransferase p300 (EP300) . Q09472
Transporter and channel
Click To Hide/Show 1 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Complement component 1 Q subcomponent-binding protein, mitochondrial (C1QBP) MAM33 family Q07021
Transcription factor
Click To Hide/Show 1 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Pituitary homeobox 2 (PITX2) Paired homeobox family Q99697
Other
Click To Hide/Show 4 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
U6 snRNA-associated Sm-like protein LSm3 (LSM3) SnRNP Sm proteins family P62310
Translationally-controlled tumor protein (TPT1) TCTP family P13693
F-box only protein 33 (FBXO33) . Q7Z6M2
TAR DNA-binding protein 43 (TARDBP) . Q13148

References

1 2-Ethynylbenzaldehyde-Based, Lysine-Targeting Irreversible Covalent Inhibitors for Protein Kinases and Nonkinases. J Am Chem Soc. 2023 Feb 12. doi: 10.1021/jacs.2c11595. Online ahead of print.
Mass spectrometry data entry: PXD037665
2 2H-Azirine-Based Reagents for Chemoselective Bioconjugation at Carboxyl Residues Inside Live Cells. J Am Chem Soc. 2020 Apr 1;142(13):6051-6059. doi: 10.1021/jacs.9b12116. Epub 2020 Mar 23.
3 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.
4 A chemical proteomics approach for global mapping of functional lysines on cell surface of living cell. Nat Commun. 2024 Apr 8;15(1):2997. doi: 10.1038/s41467-024-47033-w.
Mass spectrometry data entry: PXD042888
5 An Azo Coupling-Based Chemoproteomic Approach to Systematically Profile the Tyrosine Reactivity in the Human Proteome. Anal Chem. 2021 Jul 27;93(29):10334-10342. doi: 10.1021/acs.analchem.1c01935. Epub 2021 Jul 12.
6 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.
7 Discovery of a Cell-Active SuTEx Ligand of Prostaglandin Reductase 2. Chembiochem. 2021 Jun 15;22(12):2134-2139. doi: 10.1002/cbic.202000879. Epub 2021 Apr 29.
8 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.
9 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.
10 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.
11 A modification-centric assessment tool for the performance of chemoproteomic probes. Nat Chem Biol. 2022 Aug;18(8):904-912. doi: 10.1038/s41589-022-01074-8. Epub 2022 Jul 21.
Mass spectrometry data entry: PXD027758 , PXD027755 , PXD027760 , PXD027762 , PXD027756 , PXD027591 , PXD007149 , PXD030064 , PXD032392 , PXD027789 , PXD027767 , PXD027764
12 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
13 Oxidative cyclization reagents reveal tryptophan cation- interactions. Nature. 2024 Mar;627(8004):680-687. doi: 10.1038/s41586-024-07140-6. Epub 2024 Mar 6.
Mass spectrometry data entry: PXD001377 , PXD005252
14 Global profiling identifies a stress-responsive tyrosine site on EDC3 regulating biomolecular condensate formation. Cell Chem Biol. 2022 Dec 15;29(12):1709-1720.e7. doi: 10.1016/j.chembiol.2022.11.008. Epub 2022 Dec 6.
Mass spectrometry data entry: PXD038010
15 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
16 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.
17 Cell-based proteome profiling of potential dasatinib targets by use of affinity-based probes. J Am Chem Soc. 2012 Feb 15;134(6):3001-14. doi: 10.1021/ja208518u. Epub 2012 Feb 1.
18 Proteome profiling reveals potential cellular targets of staurosporine using a clickable cell-permeable probe. Chem Commun (Camb). 2011 Oct 28;47(40):11306-8. doi: 10.1039/c1cc14824a. Epub 2011 Sep 16.