General Information of Target

Target ID LDTP04401
Target Name Ras-related protein Rab-13 (RAB13)
Gene Name RAB13
Gene ID 5872
Synonyms
Ras-related protein Rab-13; Cell growth-inhibiting gene 4 protein
3D Structure
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2D Sequence (FASTA)
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3D Structure (PDB)
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Sequence
MAKAYDHLFKLLLIGDSGVGKTCLIIRFAEDNFNNTYISTIGIDFKIRTVDIEGKKIKLQ
VWDTAGQERFKTITTAYYRGAMGIILVYDITDEKSFENIQNWMKSIKENASAGVERLLLG
NKCDMEAKRKVQKEQADKLAREHGIRFFETSAKSSMNVDEAFSSLARDILLKSGGRRSGN
GNKPPSTDLKTCDKKNTNKCSLG
Target Bioclass
Enzyme
Family
Small GTPase superfamily, Rab family
Subcellular location
Cell membrane
Function
The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. That Rab is involved in endocytic recycling and regulates the transport to the plasma membrane of transmembrane proteins like the tight junction protein OCLN/occludin. Thereby, it regulates the assembly and the activity of tight junctions. Moreover, it may also regulate tight junction assembly by activating the PKA signaling pathway and by reorganizing the actin cytoskeleton through the activation of the downstream effectors PRKACA and MICALL2 respectively. Through its role in tight junction assembly, may play a role in the establishment of Sertoli cell barrier. Plays also a role in angiogenesis through regulation of endothelial cells chemotaxis. Also involved in neurite outgrowth. Has also been proposed to play a role in post-Golgi membrane trafficking from the TGN to the recycling endosome. Finally, it has been involved in insulin-induced transport to the plasma membrane of the glucose transporter GLUT4 and therefore may play a role in glucose homeostasis.
Uniprot ID
P51153
Ensemble ID
ENST00000368575.5
HGNC ID
HGNC:9762

Probe(s) Labeling This Target

ABPP Probe
Click To Hide/Show 22 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
m-APA
 Probe Info 
15.00  LDD0402  [1]
ONAyne
 Probe Info 
N.A.  LDD0273  [2]
OPA-S-S-alkyne
 Probe Info 
K107(0.52); K172(4.07); K58(13.17)  LDD3494  [3]
Alkylaryl probe 2
 Probe Info 
3.00  LDD0390  [4]
DBIA
 Probe Info 
C123(4.09)  LDD3311  [5]
JZ128-DTB
 Probe Info 
N.A.  LDD0462  [6]
BTD
 Probe Info 
C123(1.21)  LDD1700  [7]
DA-P3
 Probe Info 
4.18  LDD0180  [8]
EA-probe
 Probe Info 
N.A.  LDD0440  [9]
HHS-475
 Probe Info 
Y5(0.51)  LDD0264  [10]
IA-alkyne
 Probe Info 
N.A.  LDD0162  [11]
IPM
 Probe Info 
C192(0.00); C123(0.00)  LDD0025  [12]
NAIA_4
 Probe Info 
N.A.  LDD2226  [13]
NHS
 Probe Info 
K107(0.00); K58(0.00)  LDD0010  [14]
PF-06672131
 Probe Info 
N.A.  LDD0152  [15]
SF
 Probe Info 
Y78(0.00); Y5(0.00); Y77(0.00)  LDD0028  [16]
STPyne
 Probe Info 
N.A.  LDD0009  [14]
TFBX
 Probe Info 
N.A.  LDD0148  [12]
Phosphinate-6
 Probe Info 
N.A.  LDD0018  [17]
1c-yne
 Probe Info 
N.A.  LDD0228  [18]
AOyne
 Probe Info 
13.00  LDD0443  [19]
NAIA_5
 Probe Info 
C123(0.00); C192(0.00)  LDD2223  [13]

Competitor(s) Related to This Target

Competitor ID Name Cell line Binding Site(Ratio) Interaction ID Ref
 LDCM0548  1-(4-(Benzo[d][1,3]dioxol-5-ylmethyl)piperazin-1-yl)-2-nitroethan-1-one MDA-MB-231 C123(0.77)  LDD2142  [7]
 LDCM0519  1-(6-methoxy-3,4-dihydroquinolin-1(2H)-yl)-2-nitroethan-1-one MDA-MB-231 C123(0.78)  LDD2112  [7]
 LDCM0502  1-(Cyanoacetyl)piperidine MDA-MB-231 C123(0.59)  LDD2095  [7]
 LDCM0537  2-Cyano-N,N-dimethylacetamide MDA-MB-231 C123(0.91)  LDD2130  [7]
 LDCM0524  2-Cyano-N-(2-morpholin-4-yl-ethyl)-acetamide MDA-MB-231 C123(0.94)  LDD2117  [7]
 LDCM0558  2-Cyano-N-phenylacetamide MDA-MB-231 C123(1.20)  LDD2152  [7]
 LDCM0510  3-(4-(Hydroxydiphenylmethyl)piperidin-1-yl)-3-oxopropanenitrile MDA-MB-231 C123(1.06)  LDD2103  [7]
 LDCM0539  3-(4-Isopropylpiperazin-1-yl)-3-oxopropanenitrile MDA-MB-231 C123(0.59)  LDD2132  [7]
 LDCM0538  4-(Cyanoacetyl)morpholine MDA-MB-231 C123(0.67)  LDD2131  [7]
 LDCM0520  AKOS000195272 MDA-MB-231 C123(0.62)  LDD2113  [7]
 LDCM0156  Aniline NCI-H1299 12.07  LDD0403  [1]
 LDCM0498  BS-3668 MDA-MB-231 C123(0.63)  LDD2091  [7]
 LDCM0632  CL-Sc Hep-G2 C192(0.47); C123(0.25)  LDD2227  [13]
 LDCM0028  Dobutamine HEK-293T 4.18  LDD0180  [8]
 LDCM0175  Ethacrynic acid HeLa N.A.  LDD0440  [9]
 LDCM0116  HHS-0101 DM93 Y5(0.51)  LDD0264  [10]
 LDCM0117  HHS-0201 DM93 Y5(0.43)  LDD0265  [10]
 LDCM0118  HHS-0301 DM93 Y5(0.85)  LDD0266  [10]
 LDCM0119  HHS-0401 DM93 Y5(0.59)  LDD0267  [10]
 LDCM0120  HHS-0701 DM93 Y5(1.05)  LDD0268  [10]
 LDCM0179  JZ128 PC-3 N.A.  LDD0462  [6]
 LDCM0022  KB02 697 C123(2.40)  LDD2245  [5]
 LDCM0023  KB03 697 C123(3.69)  LDD2662  [5]
 LDCM0024  KB05 G361 C123(4.09)  LDD3311  [5]
 LDCM0509  N-(4-bromo-3,5-dimethylphenyl)-2-nitroacetamide MDA-MB-231 C123(1.14)  LDD2102  [7]
 LDCM0496  Nucleophilic fragment 11a MDA-MB-231 C123(0.63)  LDD2089  [7]
 LDCM0497  Nucleophilic fragment 11b MDA-MB-231 C123(0.92)  LDD2090  [7]
 LDCM0499  Nucleophilic fragment 12b MDA-MB-231 C123(0.97)  LDD2092  [7]
 LDCM0500  Nucleophilic fragment 13a MDA-MB-231 C123(1.17)  LDD2093  [7]
 LDCM0501  Nucleophilic fragment 13b MDA-MB-231 C123(1.29)  LDD2094  [7]
 LDCM0505  Nucleophilic fragment 15b MDA-MB-231 C123(0.72)  LDD2098  [7]
 LDCM0506  Nucleophilic fragment 16a MDA-MB-231 C123(1.05)  LDD2099  [7]
 LDCM0507  Nucleophilic fragment 16b MDA-MB-231 C123(0.80)  LDD2100  [7]
 LDCM0512  Nucleophilic fragment 19a MDA-MB-231 C123(1.53)  LDD2105  [7]
 LDCM0513  Nucleophilic fragment 19b MDA-MB-231 C123(0.84)  LDD2106  [7]
 LDCM0514  Nucleophilic fragment 20a MDA-MB-231 C123(0.88)  LDD2107  [7]
 LDCM0515  Nucleophilic fragment 20b MDA-MB-231 C123(0.68)  LDD2108  [7]
 LDCM0516  Nucleophilic fragment 21a MDA-MB-231 C123(0.87)  LDD2109  [7]
 LDCM0518  Nucleophilic fragment 22a MDA-MB-231 C123(1.05)  LDD2111  [7]
 LDCM0521  Nucleophilic fragment 23b MDA-MB-231 C123(0.94)  LDD2114  [7]
 LDCM0525  Nucleophilic fragment 25b MDA-MB-231 C123(0.75)  LDD2118  [7]
 LDCM0526  Nucleophilic fragment 26a MDA-MB-231 C123(1.67)  LDD2119  [7]
 LDCM0527  Nucleophilic fragment 26b MDA-MB-231 C123(1.04)  LDD2120  [7]
 LDCM0529  Nucleophilic fragment 27b MDA-MB-231 C123(0.33)  LDD2122  [7]
 LDCM0531  Nucleophilic fragment 28b MDA-MB-231 C123(1.02)  LDD2124  [7]
 LDCM0532  Nucleophilic fragment 29a MDA-MB-231 C123(0.93)  LDD2125  [7]
 LDCM0533  Nucleophilic fragment 29b MDA-MB-231 C123(1.20)  LDD2126  [7]
 LDCM0534  Nucleophilic fragment 30a MDA-MB-231 C123(1.15)  LDD2127  [7]
 LDCM0535  Nucleophilic fragment 30b MDA-MB-231 C123(1.20)  LDD2128  [7]
 LDCM0536  Nucleophilic fragment 31 MDA-MB-231 C123(1.02)  LDD2129  [7]
 LDCM0540  Nucleophilic fragment 35 MDA-MB-231 C123(0.66)  LDD2133  [7]
 LDCM0542  Nucleophilic fragment 37 MDA-MB-231 C123(1.08)  LDD2135  [7]
 LDCM0211  Nucleophilic fragment 3b MDA-MB-231 C123(1.21)  LDD1700  [7]
 LDCM0546  Nucleophilic fragment 40 MDA-MB-231 C123(0.83)  LDD2140  [7]
 LDCM0547  Nucleophilic fragment 41 MDA-MB-231 C123(0.62)  LDD2141  [7]
 LDCM0549  Nucleophilic fragment 43 MDA-MB-231 C123(1.04)  LDD2143  [7]
 LDCM0550  Nucleophilic fragment 5a MDA-MB-231 C123(2.13)  LDD2144  [7]
 LDCM0552  Nucleophilic fragment 6a MDA-MB-231 C123(0.88)  LDD2146  [7]
 LDCM0553  Nucleophilic fragment 6b MDA-MB-231 C123(2.58)  LDD2147  [7]
 LDCM0556  Nucleophilic fragment 8a MDA-MB-231 C123(0.50)  LDD2150  [7]
 LDCM0628  OTUB2-COV-1 HEK-293T C192(1.10); C123(1.07)  LDD2207  [20]
 LDCM0099  Phenelzine HEK-293T 3.00  LDD0390  [4]

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
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (PDE6D) PDE6D/unc-119 family O43924

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 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
3 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
4 Hydrazines as versatile chemical biology probes and drug-discovery tools for cofactor-dependent enzymes. bioRxiv, 2020-06.
5 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
6 A Chemoproteomic Strategy for Direct and Proteome-Wide Covalent Inhibitor Target-Site Identification. J Am Chem Soc. 2019 Jan 9;141(1):191-203. doi: 10.1021/jacs.8b07911. Epub 2018 Dec 20.
7 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
8 A chemical probe unravels the reactive proteome of health-associated catechols. Chem Sci. 2023 Jul 22;14(32):8635-8643. doi: 10.1039/d3sc00888f. eCollection 2023 Aug 16.
Mass spectrometry data entry: PXD043348
9 Chemoproteomic Profiling Reveals Ethacrynic Acid Targets Adenine Nucleotide Translocases to Impair Mitochondrial Function. Mol Pharm. 2018 Jun 4;15(6):2413-2422. doi: 10.1021/acs.molpharmaceut.8b00250. Epub 2018 May 15.
10 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.
11 SP3-FAIMS Chemoproteomics for High-Coverage Profiling of the Human Cysteinome*. Chembiochem. 2021 May 14;22(10):1841-1851. doi: 10.1002/cbic.202000870. Epub 2021 Feb 18.
Mass spectrometry data entry: PXD023056 , PXD023059 , PXD023058 , PXD023057 , PXD023060
12 Chemoproteomic Profiling by Cysteine Fluoroalkylation Reveals Myrocin G as an Inhibitor of the Nonhomologous End Joining DNA Repair Pathway. J Am Chem Soc. 2021 Dec 8;143(48):20332-20342. doi: 10.1021/jacs.1c09724. Epub 2021 Nov 24.
Mass spectrometry data entry: PXD029255
13 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
14 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
15 Site-Specific Activity-Based Protein Profiling Using Phosphonate Handles. Mol Cell Proteomics. 2023 Jan;22(1):100455. doi: 10.1016/j.mcpro.2022.100455. Epub 2022 Nov 24.
Mass spectrometry data entry: PXD036569
16 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
17 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
18 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.
19 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.
20 Rapid Covalent-Probe Discovery by Electrophile-Fragment Screening. J Am Chem Soc. 2019 Jun 5;141(22):8951-8968. doi: 10.1021/jacs.9b02822. Epub 2019 May 22.