Details of the Target

General Information of Target

Target ID LDTP03354
Target Name Large ribosomal subunit protein eL13 (RPL13)
Gene Name RPL13
Gene ID 6137
Synonyms
BBC1; Large ribosomal subunit protein eL13; 60S ribosomal protein L13; Breast basic conserved protein 1
3D Structure
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2D Sequence (FASTA)
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3D Structure (PDB)
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Sequence
MAPSRNGMVLKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPVRNVYKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK
Target Bioclass
Other
Family
Eukaryotic ribosomal protein eL13 family
Subcellular location
Cytoplasm
Function
Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules (Probable). The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain (Probable). The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel (Probable). As part of the LSU, it is probably required for its formation and the maturation of rRNAs. Plays a role in bone development.
Uniprot ID
P26373
Ensemble ID
ENST00000311528.10
HGNC ID
HGNC:10303

Target Site Mutations in Different Cell Lines

Cell line Mutation details Probe for labeling this protein in this cell
IM95 SNV: p.R186C DBIA    Probe Info 
JHH1 SNV: p.N113S .
NCIH2172 SNV: p.F179L .

Probe(s) Labeling This Target

ABPP Probe
Click To Hide/Show 23 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
m-APA
 Probe Info  		8.44  LDD0402  [1]
A-EBA
 Probe Info  		3.15  LDD0215  [2]
C-Sul
 Probe Info  		4.78  LDD0066  [3]
YN-4
 Probe Info  		100.00  LDD0445  [4]
STPyne
 Probe Info  		K123(8.50); K145(7.63); K163(1.10); K174(6.25)  LDD0277  [5]
ONAyne
 Probe Info  		K177(0.00); K69(0.00); K200(0.00); K105(0.00)  LDD0273  [5]
AF-1
 Probe Info  		1.54  LDD0421  [6]
DBIA
 Probe Info  		C186(1.85)  LDD2356  [7]
AZ-9
 Probe Info  		8.02  LDD2154  [8]
W1
 Probe Info  		S122(0.94)  LDD0239  [9]
AMP probe
 Probe Info  		N.A.  LDD0200  [10]
ATP probe
 Probe Info  		K200(0.00); K136(0.00); K174(0.00); K177(0.00)  LDD0199  [10]
ATP probe
 Probe Info  		K136(0.00); K200(0.00); K11(0.00)  LDD0035  [11]
1d-yne
 Probe Info  		N.A.  LDD0356  [12]
NHS
 Probe Info  		K177(0.00); K145(0.00)  LDD0010  [13]
OSF
 Probe Info  		N.A.  LDD0029  [14]
SF
 Probe Info  		K88(0.00); K130(0.00); K123(0.00); K177(0.00)  LDD0028  [14]
Phosphinate-6
 Probe Info  		N.A.  LDD0018  [15]
Ox-W18
 Probe Info  		N.A.  LDD2175  [16]
1c-yne
 Probe Info  		N.A.  LDD0228  [12]
Acrolein
 Probe Info  		H13(0.00); H15(0.00)  LDD0217  [17]
AOyne
 Probe Info  		6.10  LDD0443  [18]
MPP-AC
 Probe Info  		N.A.  LDD0428  [19]
PAL-AfBPP Probe
Click To Hide/Show 1 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
DA-2
 Probe Info  		N.A.  LDD0072  [20]

Competitor(s) Related to This Target

Competitor ID Name Cell line Binding Site(Ratio) Interaction ID Ref
 LDCM0166  Afatinib A431 1.54  LDD0421  [6]
 LDCM0151  AZ-11 HeLa 8.02  LDD2154  [8]
 LDCM0108  Chloroacetamide HeLa H13(0.00); H15(0.00)  LDD0222  [17]
 LDCM0107  IAA HeLa H13(0.00); H15(0.00)  LDD0221  [17]
 LDCM0022  KB02 HGC-27 C186(1.85)  LDD2356  [7]
 LDCM0023  KB03 HGC-27 C186(1.82)  LDD2773  [7]
 LDCM0024  KB05 HGC-27 C186(2.06)  LDD3190  [7]
 LDCM0109  NEM HeLa H13(0.00); H15(0.00)  LDD0223  [17]
 LDCM0112  W16 Hep-G2 S122(0.94)  LDD0239  [9]
 LDCM0113  W17 Hep-G2 S122(0.59); K123(0.62)  LDD0240  [9]

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
Leucine-rich repeat serine/threonine-protein kinase 2 (LRRK2) TKL Ser/Thr protein kinase family Q5S007
Transporter and channel
Click To Hide/Show 1 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Huntingtin (HTT) Huntingtin family P42858
Other
Click To Hide/Show 5 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Large ribosomal subunit protein mL38 (MRPL38) Phosphatidylethanolamine-binding protein family Q96DV4
Phosphatidylinositol 3-kinase regulatory subunit alpha (PIK3R1) PI3K p85 subunit family P27986
Centrosomal protein of 70 kDa (CEP70) . Q8NHQ1
SH2/SH3 adapter protein NCK1 (NCK1) . P16333
Telomeric repeat-binding factor 2 (TERF2) . Q15554

References

1 Quantitative and Site-Specific Chemoproteomic Profiling of Targets of Acrolein. Chem Res Toxicol. 2019 Mar 18;32(3):467-473. doi: 10.1021/acs.chemrestox.8b00343. Epub 2019 Jan 15.
2 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
3 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.
4 Ynamide Electrophile for the Profiling of Ligandable Carboxyl Residues in Live Cells and the Development of New Covalent Inhibitors. J Med Chem. 2022 Aug 11;65(15):10408-10418. doi: 10.1021/acs.jmedchem.2c00272. Epub 2022 Jul 26.
5 A Paal-Knorr agent for chemoproteomic profiling of targets of isoketals in cells. Chem Sci. 2021 Oct 15;12(43):14557-14563. doi: 10.1039/d1sc02230j. eCollection 2021 Nov 10.
Mass spectrometry data entry: PXD028270
6 Minimalist linkers suitable for irreversible inhibitors in simultaneous proteome profiling, live-cell imaging and drug screening. Chem Commun (Camb). 2019 Jan 15;55(6):834-837. doi: 10.1039/c8cc08685k.
7 DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. Cell. 2024 May 9;187(10):2536-2556.e30. doi: 10.1016/j.cell.2024.03.027. Epub 2024 Apr 22.
Mass spectrometry data entry: PXD047840
8 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.
9 Oxidant-Induced Bioconjugation for Protein Labeling in Live Cells. ACS Chem Biol. 2023 Jan 20;18(1):112-122. doi: 10.1021/acschembio.2c00740. Epub 2022 Dec 21.
10 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.
11 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
12 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.
13 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
14 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
15 DFT-Guided Discovery of Ethynyl-Triazolyl-Phosphinates as Modular Electrophiles for Chemoselective Cysteine Bioconjugation and Profiling. Angew Chem Int Ed Engl. 2022 Oct 10;61(41):e202205348. doi: 10.1002/anie.202205348. Epub 2022 Aug 22.
Mass spectrometry data entry: PXD033004
16 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
17 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.
18 Chemoproteomic profiling of targets of lipid-derived electrophiles by bioorthogonal aminooxy probe. Redox Biol. 2017 Aug;12:712-718. doi: 10.1016/j.redox.2017.04.001. Epub 2017 Apr 5.
19 Differently Tagged Probes for Protein Profiling of Mitochondria. Chembiochem. 2019 May 2;20(9):1155-1160. doi: 10.1002/cbic.201800735. Epub 2019 Mar 26.
20 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.