Details of the Target

General Information of Target

Target ID LDTP11046
Target Name RNA-binding protein 4B (RBM4B)
Gene Name RBM4B
Gene ID 83759
Synonyms
RBM30; RNA-binding protein 4B; RNA-binding motif protein 30; RNA-binding motif protein 4B; RNA-binding protein 30
3D Structure
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2D Sequence (FASTA)
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3D Structure (PDB)
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Sequence
MAFLDNPTIILAHIRQSHVTSDDTGMCEMVLIDHDVDLEKIHPPSMPGDSGSEIQGSNGE
TQGYVYAQSVDITSSWDFGIRRRSNTAQRLERLRKERQNQIKCKNIQWKERNSKQSAQEL
KSLFEKKSLKEKPPISGKQSILSVRLEQCPLQLNNPFNEYSKFDGKGHVGTTATKKIDVY
LPLHSSQDRLLPMTVVTMASARVQDLIGLICWQYTSEGREPKLNDNVSAYCLHIAEDDGE
VDTDFPPLDSNEPIHKFGFSTLALVEKYSSPGLTSKESLFVRINAAHGFSLIQVDNTKVT
MKEILLKAVKRRKGSQKVSGPQYRLEKQSEPNVAVDLDSTLESQSAWEFCLVRENSSRAD
GVFEEDSQIDIATVQDMLSSHHYKSFKVSMIHRLRFTTDVQLGISGDKVEIDPVTNQKAS
TKFWIKQKPISIDSDLLCACDLAEEKSPSHAIFKLTYLSNHDYKHLYFESDAATVNEIVL
KVNYILESRASTARADYFAQKQRKLNRRTSFSFQKEKKSGQQ
Target Bioclass
Other
Subcellular location
Nucleus
Function Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA.
Uniprot ID
Q9BQ04
Ensemble ID
ENST00000310046.9
HGNC ID
HGNC:28842

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
STPyne
 Probe Info  		K3(8.33)  LDD0277  [1]
IPM
 Probe Info  		C31(0.00); C162(0.00); C107(0.00); C89(0.00)  LDD0241  [2]
Probe 1
 Probe Info  		Y25(43.87); Y101(16.16); Y194(13.00); Y320(8.66)  LDD3495  [3]
DBIA
 Probe Info  		C107(1.56); C31(1.34)  LDD3312  [4]
BTD
 Probe Info  		C31(0.65)  LDD2090  [5]
AHL-Pu-1
 Probe Info  		C107(2.36)  LDD0168  [6]
HPAP
 Probe Info  		3.75  LDD0062  [7]
HHS-465
 Probe Info  		Y37(6.87); Y58(10.00)  LDD2237  [8]
ATP probe
 Probe Info  		K71(0.00); K3(0.00); K35(0.00); K79(0.00)  LDD0199  [9]
4-Iodoacetamidophenylacetylene
 Probe Info  		N.A.  LDD0038  [10]
IA-alkyne
 Probe Info  		N.A.  LDD0036  [10]
WYneN
 Probe Info  		C31(0.00); C162(0.00)  LDD0021  [11]
WYneO
 Probe Info  		N.A.  LDD0022  [11]
NHS
 Probe Info  		N.A.  LDD0010  [11]
Phosphinate-6
 Probe Info  		C175(0.00); C162(0.00); C165(0.00); C31(0.00)  LDD0018  [12]
Acrolein
 Probe Info  		H41(0.00); C31(0.00); C89(0.00); C107(0.00)  LDD0217  [13]
Crotonaldehyde
 Probe Info  		N.A.  LDD0219  [13]
Methacrolein
 Probe Info  		N.A.  LDD0218  [13]
NAIA_5
 Probe Info  		C107(0.00); C165(0.00); C89(0.00); C162(0.00)  LDD2223  [14]
PAL-AfBPP Probe
Click To Hide/Show 5 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
FFF probe11
 Probe Info  		8.16  LDD0471  [15]
FFF probe13
 Probe Info  		16.95  LDD0475  [15]
FFF probe2
 Probe Info  		16.98  LDD0463  [15]
FFF probe3
 Probe Info  		13.29  LDD0464  [15]
FFF probe6
 Probe Info  		20.00  LDD0467  [15]

Competitor(s) Related to This Target

Competitor ID Name Cell line Binding Site(Ratio) Interaction ID Ref
 LDCM0519  1-(6-methoxy-3,4-dihydroquinolin-1(2H)-yl)-2-nitroethan-1-one MDA-MB-231 C31(0.65)  LDD2112  [5]
 LDCM0524  2-Cyano-N-(2-morpholin-4-yl-ethyl)-acetamide MDA-MB-231 C31(1.04); C89(0.81)  LDD2117  [5]
 LDCM0510  3-(4-(Hydroxydiphenylmethyl)piperidin-1-yl)-3-oxopropanenitrile MDA-MB-231 C31(0.96)  LDD2103  [5]
 LDCM0025  4SU-RNA HEK-293T C107(2.36)  LDD0168  [6]
 LDCM0026  4SU-RNA+native RNA HEK-293T C107(2.73)  LDD0169  [6]
 LDCM0214  AC1 HEK-293T C89(0.75)  LDD1507  [16]
 LDCM0276  AC17 HEK-293T C89(1.07)  LDD1515  [16]
 LDCM0284  AC24 HEK-293T C89(0.89)  LDD1523  [16]
 LDCM0285  AC25 HEK-293T C89(0.90)  LDD1524  [16]
 LDCM0293  AC32 HEK-293T C89(0.89)  LDD1532  [16]
 LDCM0294  AC33 HEK-293T C89(0.82)  LDD1533  [16]
 LDCM0302  AC40 HEK-293T C89(1.07)  LDD1541  [16]
 LDCM0303  AC41 HEK-293T C89(1.06)  LDD1542  [16]
 LDCM0310  AC48 HEK-293T C89(1.05)  LDD1549  [16]
 LDCM0311  AC49 HEK-293T C89(1.04)  LDD1550  [16]
 LDCM0319  AC56 HEK-293T C89(0.99)  LDD1558  [16]
 LDCM0320  AC57 HEK-293T C89(1.30)  LDD1559  [16]
 LDCM0328  AC64 HEK-293T C89(1.09)  LDD1567  [16]
 LDCM0345  AC8 HEK-293T C89(0.87)  LDD1569  [16]
 LDCM0356  AKOS034007680 HEK-293T C89(1.10)  LDD1570  [16]
 LDCM0275  AKOS034007705 HEK-293T C89(0.99)  LDD1514  [16]
 LDCM0108  Chloroacetamide HeLa H41(0.00); C162(0.00); C107(0.00)  LDD0222  [13]
 LDCM0367  CL1 HEK-293T C89(1.13)  LDD1571  [16]
 LDCM0370  CL101 HEK-293T C89(1.05)  LDD1574  [16]
 LDCM0374  CL105 HEK-293T C89(0.97)  LDD1578  [16]
 LDCM0378  CL109 HEK-293T C89(1.06)  LDD1582  [16]
 LDCM0383  CL113 HEK-293T C89(1.12)  LDD1587  [16]
 LDCM0387  CL117 HEK-293T C89(1.13)  LDD1591  [16]
 LDCM0390  CL12 HEK-293T C89(0.84)  LDD1594  [16]
 LDCM0392  CL121 HEK-293T C89(0.91)  LDD1596  [16]
 LDCM0396  CL125 HEK-293T C89(1.00)  LDD1600  [16]
 LDCM0400  CL13 HEK-293T C89(0.96)  LDD1604  [16]
 LDCM0404  CL17 HEK-293T C89(0.96)  LDD1608  [16]
 LDCM0412  CL24 HEK-293T C89(1.03)  LDD1616  [16]
 LDCM0413  CL25 HEK-293T C89(0.88)  LDD1617  [16]
 LDCM0417  CL29 HEK-293T C89(0.89)  LDD1621  [16]
 LDCM0425  CL36 HEK-293T C89(0.99)  LDD1629  [16]
 LDCM0426  CL37 HEK-293T C89(1.10)  LDD1630  [16]
 LDCM0431  CL41 HEK-293T C89(0.93)  LDD1635  [16]
 LDCM0438  CL48 HEK-293T C89(0.99)  LDD1642  [16]
 LDCM0439  CL49 HEK-293T C89(1.05)  LDD1643  [16]
 LDCM0440  CL5 HEK-293T C89(0.89)  LDD1644  [16]
 LDCM0444  CL53 HEK-293T C89(0.82)  LDD1647  [16]
 LDCM0452  CL60 HEK-293T C89(1.27)  LDD1655  [16]
 LDCM0453  CL61 HEK-293T C89(1.01)  LDD1656  [16]
 LDCM0457  CL65 HEK-293T C89(1.01)  LDD1660  [16]
 LDCM0465  CL72 HEK-293T C89(1.00)  LDD1668  [16]
 LDCM0466  CL73 HEK-293T C89(0.96)  LDD1669  [16]
 LDCM0470  CL77 HEK-293T C89(0.80)  LDD1673  [16]
 LDCM0478  CL84 HEK-293T C89(0.90)  LDD1681  [16]
 LDCM0479  CL85 HEK-293T C89(1.09)  LDD1682  [16]
 LDCM0483  CL89 HEK-293T C89(0.76)  LDD1686  [16]
 LDCM0491  CL96 HEK-293T C89(0.90)  LDD1694  [16]
 LDCM0492  CL97 HEK-293T C89(0.89)  LDD1695  [16]
 LDCM0625  F8 Ramos C89(0.86)  LDD2187  [17]
 LDCM0576  Fragment14 Ramos C89(1.71)  LDD2193  [17]
 LDCM0586  Fragment28 Ramos C89(0.59)  LDD2198  [17]
 LDCM0566  Fragment4 Ramos C89(0.53)  LDD2184  [17]
 LDCM0569  Fragment7 Ramos C89(0.45)  LDD2186  [17]
 LDCM0107  IAA HeLa C107(0.00); H41(0.00); H117(0.00); C89(0.00)  LDD0221  [13]
 LDCM0022  KB02 HEK-293T C89(1.10)  LDD1492  [16]
 LDCM0023  KB03 HEK-293T C89(1.02)  LDD1497  [16]
 LDCM0024  KB05 HMCB C107(1.56); C31(1.34)  LDD3312  [4]
 LDCM0509  N-(4-bromo-3,5-dimethylphenyl)-2-nitroacetamide MDA-MB-231 C31(0.91)  LDD2102  [5]
 LDCM0109  NEM HeLa H41(0.00); H61(0.00); H142(0.00)  LDD0223  [13]
 LDCM0497  Nucleophilic fragment 11b MDA-MB-231 C31(0.65)  LDD2090  [5]
 LDCM0513  Nucleophilic fragment 19b MDA-MB-231 C31(0.44)  LDD2106  [5]
 LDCM0521  Nucleophilic fragment 23b MDA-MB-231 C31(1.01)  LDD2114  [5]
 LDCM0547  Nucleophilic fragment 41 MDA-MB-231 C31(0.48)  LDD2141  [5]
 LDCM0551  Nucleophilic fragment 5b MDA-MB-231 C31(2.34)  LDD2145  [5]
 LDCM0559  Nucleophilic fragment 9b MDA-MB-231 C31(0.87)  LDD2153  [5]
 LDCM0014  Panhematin HEK-293T 3.75  LDD0062  [7]

The Interaction Atlas With This Target

The Protein(s) Related To This Target

Enzyme
Click To Hide/Show 2 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Histone-lysine N-methyltransferase SMYD1 (SMYD1) Class V-like SAM-binding methyltransferase superfamily Q8NB12
E3 ubiquitin-protein ligase DZIP3 (DZIP3) . Q86Y13
Transcription factor
Click To Hide/Show 2 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Krueppel-like factor 1 (KLF1) Krueppel C2H2-type zinc-finger protein family Q13351
NF-kappa-B inhibitor delta (NFKBID) NF-kappa-B inhibitor family Q8NI38
Other
Click To Hide/Show 3 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
U1 small nuclear ribonucleoprotein A (SNRPA) RRM U1 A/B'' family P09012
Heterogeneous nuclear ribonucleoprotein U-like protein 1 (HNRNPUL1) . Q9BUJ2
Testis-specific protein 10-interacting protein (TSGA10IP) . Q3SY00

References

1 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
2 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.
3 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.
4 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
5 Nucleophilic covalent ligand discovery for the cysteine redoxome. Nat Chem Biol. 2023 Nov;19(11):1309-1319. doi: 10.1038/s41589-023-01330-5. Epub 2023 May 29.
Mass spectrometry data entry: PXD039908 , PXD029761
6 Chemoproteomic capture of RNA binding activity in living cells. Nat Commun. 2023 Oct 7;14(1):6282. doi: 10.1038/s41467-023-41844-z.
Mass spectrometry data entry: PXD044625
7 A Chemical Proteomic Map of Heme-Protein Interactions. J Am Chem Soc. 2022 Aug 24;144(33):15013-15019. doi: 10.1021/jacs.2c06104. Epub 2022 Aug 12.
Mass spectrometry data entry: PXD034651
8 Global targeting of functional tyrosines using sulfur-triazole exchange chemistry. Nat Chem Biol. 2020 Feb;16(2):150-159. doi: 10.1038/s41589-019-0404-5. Epub 2019 Nov 25.
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 Enhancing Cysteine Chemoproteomic Coverage through Systematic Assessment of Click Chemistry Product Fragmentation. Anal Chem. 2022 Mar 8;94(9):3800-3810. doi: 10.1021/acs.analchem.1c04402. Epub 2022 Feb 23.
Mass spectrometry data entry: PXD028853
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 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
13 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.
14 N-Acryloylindole-alkyne (NAIA) enables imaging and profiling new ligandable cysteines and oxidized thiols by chemoproteomics. Nat Commun. 2023 Jun 15;14(1):3564. doi: 10.1038/s41467-023-39268-w.
Mass spectrometry data entry: PXD041264
15 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.
16 Accelerating multiplexed profiling of protein-ligand interactions: High-throughput plate-based reactive cysteine profiling with minimal input. Cell Chem Biol. 2024 Mar 21;31(3):565-576.e4. doi: 10.1016/j.chembiol.2023.11.015. Epub 2023 Dec 19.
Mass spectrometry data entry: PXD044402
17 Site-specific quantitative cysteine profiling with data-independent acquisition-based mass spectrometry. Methods Enzymol. 2023;679:295-322. doi: 10.1016/bs.mie.2022.07.037. Epub 2022 Sep 7.
Mass spectrometry data entry: PXD027578