Details of the Target

General Information of Target

Target ID LDTP01659
Target Name Ras-related protein Rab-3D (RAB3D)
Gene Name RAB3D
Gene ID 9545
Synonyms
GOV; RAB16; Ras-related protein Rab-3D
3D Structure
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2D Sequence (FASTA)
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3D Structure (PDB)
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Sequence
MASAGDTQAGPRDAADQNFDYMFKLLLIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFK
VKTVYRHDKRIKLQIWDTAGQERYRTITTAYYRGAMGFLLMYDIANQESFAAVQDWATQI
KTYSWDNAQVILVGNKCDLEDERVVPAEDGRRLADDLGFEFFEASAKENINVKQVFERLV
DVICEKMNESLEPSSSSGSNGKGPAVGDAPAPQPSSCSC
Target Bioclass
Enzyme
Family
Small GTPase superfamily, Rab family
Subcellular location
Cell membrane
Function Protein transport. Probably involved in regulated exocytosis.
Uniprot ID
O95716
Ensemble ID
ENST00000222120.8
HGNC ID
HGNC:9779

Probe(s) Labeling This Target

ABPP Probe
Click To Hide/Show 12 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
1oxF11yne
 Probe Info  		N.A.  LDD0193  [1]
IPM
 Probe Info  		N.A.  LDD0241  [2]
OPA-S-S-alkyne
 Probe Info  		K72(2.18)  LDD3494  [3]
DBIA
 Probe Info  		C184(3.26)  LDD3312  [4]
BTD
 Probe Info  		C184(1.87)  LDD2099  [5]
4-Iodoacetamidophenylacetylene
 Probe Info  		N.A.  LDD0038  [6]
IA-alkyne
 Probe Info  		N.A.  LDD0036  [6]
PF-06672131
 Probe Info  		N.A.  LDD0152  [7]
TFBX
 Probe Info  		C184(0.00); C137(0.00)  LDD0148  [8]
Acrolein
 Probe Info  		C137(0.00); C184(0.00)  LDD0217  [9]
W1
 Probe Info  		N.A.  LDD0236  [2]
NAIA_5
 Probe Info  		N.A.  LDD2223  [10]
PAL-AfBPP Probe
Click To Hide/Show 1 Probe Related to This Target
Probe name Structure Binding Site(Ratio) Interaction ID Ref
C235
 Probe Info  		18.00  LDD1908  [11]

Competitor(s) Related to This Target

Competitor ID Name Cell line Binding Site(Ratio) Interaction ID Ref
 LDCM0108  Chloroacetamide HeLa C184(0.00); C137(0.00)  LDD0222  [9]
 LDCM0632  CL-Sc Hep-G2 C184(1.25)  LDD2227  [10]
 LDCM0625  F8 Ramos C184(0.78)  LDD2187  [12]
 LDCM0572  Fragment10 Ramos C184(0.63)  LDD2189  [12]
 LDCM0573  Fragment11 Ramos C184(17.35)  LDD2190  [12]
 LDCM0574  Fragment12 Ramos C184(0.60)  LDD2191  [12]
 LDCM0575  Fragment13 Ramos C184(0.93)  LDD2192  [12]
 LDCM0576  Fragment14 Ramos C184(0.72)  LDD2193  [12]
 LDCM0579  Fragment20 Ramos C184(0.56)  LDD2194  [12]
 LDCM0580  Fragment21 Ramos C184(0.82)  LDD2195  [12]
 LDCM0582  Fragment23 Ramos C184(1.16)  LDD2196  [12]
 LDCM0578  Fragment27 Ramos C184(0.72)  LDD2197  [12]
 LDCM0586  Fragment28 Ramos C184(0.77)  LDD2198  [12]
 LDCM0588  Fragment30 Ramos C184(0.91)  LDD2199  [12]
 LDCM0589  Fragment31 Ramos C184(1.00)  LDD2200  [12]
 LDCM0590  Fragment32 Ramos C184(0.48)  LDD2201  [12]
 LDCM0468  Fragment33 Ramos C184(0.79)  LDD2202  [12]
 LDCM0596  Fragment38 Ramos C184(1.05)  LDD2203  [12]
 LDCM0566  Fragment4 Ramos C184(0.81)  LDD2184  [12]
 LDCM0610  Fragment52 Ramos C184(0.85)  LDD2204  [12]
 LDCM0614  Fragment56 Ramos C184(1.13)  LDD2205  [12]
 LDCM0569  Fragment7 Ramos C184(0.67)  LDD2186  [12]
 LDCM0571  Fragment9 Ramos C184(0.62)  LDD2188  [12]
 LDCM0107  IAA HeLa C184(0.00); C137(0.00)  LDD0221  [9]
 LDCM0022  KB02 Ramos C184(0.70)  LDD2182  [12]
 LDCM0023  KB03 Ramos C184(0.91)  LDD2183  [12]
 LDCM0024  KB05 HMCB C184(3.26)  LDD3312  [4]
 LDCM0506  Nucleophilic fragment 16a MDA-MB-231 C184(1.87)  LDD2099  [5]
 LDCM0514  Nucleophilic fragment 20a MDA-MB-231 C184(1.26)  LDD2107  [5]
 LDCM0516  Nucleophilic fragment 21a MDA-MB-231 C184(0.56)  LDD2109  [5]
 LDCM0518  Nucleophilic fragment 22a MDA-MB-231 C184(1.41)  LDD2111  [5]
 LDCM0522  Nucleophilic fragment 24a MDA-MB-231 C184(0.74)  LDD2115  [5]
 LDCM0530  Nucleophilic fragment 28a MDA-MB-231 C184(0.99)  LDD2123  [5]
 LDCM0532  Nucleophilic fragment 29a MDA-MB-231 C184(1.00)  LDD2125  [5]
 LDCM0534  Nucleophilic fragment 30a MDA-MB-231 C184(1.51)  LDD2127  [5]
 LDCM0542  Nucleophilic fragment 37 MDA-MB-231 C184(1.46)  LDD2135  [5]
 LDCM0543  Nucleophilic fragment 38 MDA-MB-231 C184(1.49)  LDD2136  [5]
 LDCM0546  Nucleophilic fragment 40 MDA-MB-231 C184(1.44)  LDD2140  [5]

The Interaction Atlas With This Target

The Protein(s) Related To This Target

Transporter and channel
Click To Hide/Show 1 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Synaptotagmin-like protein 4 (SYTL4) . Q96C24
Other
Click To Hide/Show 2 Protein(s) Interacting with This Target
Protein name Family Uniprot ID
Guanine nucleotide exchange factor MSS4 (RABIF) DSS4/MSS4 family P47224
Vertnin (VRTN) Vertnin family Q9H8Y1

References

1 An Activity-Based Oxaziridine Platform for Identifying and Developing Covalent Ligands for Functional Allosteric Methionine Sites: Redox-Dependent Inhibition of Cyclin-Dependent Kinase 4. J Am Chem Soc. 2022 Dec 21;144(50):22890-22901. doi: 10.1021/jacs.2c04039. Epub 2022 Dec 9.
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 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 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 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
7 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
8 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
9 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.
10 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
11 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
12 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