Target Information
| Target General Information | Top | |||||
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| Target ID |
T56871
(Former ID: TTDI00137)
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| Target Name |
Lysine-specific demethylase 5B (KDM5B)
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| Synonyms |
Retinoblastomabinding protein 2 homolog 1; Retinoblastoma-binding protein 2 homolog 1; RBP2H1; RBP2-H1; RBBP2H1; PLU1; PLU-1; Lysinespecific demethylase 5B; Jumonji/ARID domaincontaining protein 1B; Jumonji/ARID domain-containing protein 1B; JARID1B; Histone demethylase JARID1B; Cancer/testis antigen 31; CT31
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| Gene Name |
KDM5B
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| Target Type |
Literature-reported target
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| Function |
Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor suppressor genes such as BRCA1 and HOXA5. In contrast, may act as a tumor suppressor for melanoma. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2. Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code.
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| BioChemical Class |
Paired donor oxygen oxidoreductase
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| UniProt ID | ||||||
| EC Number |
EC 1.14.11.-
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| Sequence |
MEAATTLHPGPRPALPLGGPGPLGEFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTG
ICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLNFLDQIAKYWELQGSTLKI PHVERKILDLFQLNKLVAEEGGFAVVCKDRKWTKIATKMGFAPGKAVGSHIRGHYERILN PYNLFLSGDSLRCLQKPNLTTDTKDKEYKPHDIPQRQSVQPSETCPPARRAKRMRAEAMN IKIEPEETTEARTHNLRRRMGCPTPKCENEKEMKSSIKQEPIERKDYIVENEKEKPKSRS KKATNAVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE CSKPQEAFGFEQAARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEED VTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADIC GMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPE LFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAV NFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIE DEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVK ELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKINKKKSLVSFK ALIEESEMKKFPDNDLLRHLRLVTQDAEKCASVAQQLLNGKRQTRYRSGGGKSQNQLTVN ELRQFVTQLYALPCVLSQTPLLKDLLNRVEDFQQHSQKLLSEETPSAAELQDLLDVSFEF DVELPQLAEMRIRLEQARWLEEVQQACLDPSSLTLDDMRRLIDLGVGLAPYSAVEKAMAR LQELLTVSEHWDDKAKSLLKARPRHSLNSLATAVKEIEEIPAYLPNGAALKDSVQRARDW LQDVEGLQAGGRVPVLDTLIELVTRGRSIPVHLNSLPRLETLVAEVQAWKECAVNTFLTE NSPYSLLEVLCPRCDIGLLGLKRKQRKLKEPLPNGKKKSTKLESLSDLERALTESKETAS AMATLGEARLREMEALQSLRLANEGKLLSPLQDVDIKICLCQKAPAAPMIQCELCRDAFH TSCVAVPSISQGLRIWLCPHCRRSEKPPLEKILPLLASLQRIRVRLPEGDALRYMIERTV NWQHRAQQLLSSGNLKFVQDRVGSGLLYSRWQASAGQVSDTNKVSQPPGTTSFSLPDDWD NRTSYLHSPFSTGRSCIPLHGVSPEVNELLMEAQLLQVSLPEIQELYQTLLAKPSPAQQT DRSSPVRPSSEKNDCCRGKRDGINSLERKLKRRLEREGLSSERWERVKKMRTPKKKKIKL SHPKDMNNFKLERERSYELVRSAETHSLPSDTSYSEQEDSEDEDAICPAVSCLQPEGDEV DWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCTVKDAPSRK Click to Show/Hide
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| 3D Structure | Click to Show 3D Structure of This Target | AlphaFold | ||||
| Cell-based Target Expression Variations | Top | |||||
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| Cell-based Target Expression Variations | ||||||
| Drug Binding Sites of Target | Top | |||||
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| Ligand Name: Pyruvic acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with pyruvate | PDB:5FY9 | ||||
| Method | X-ray diffraction | Resolution | 2.03 Å | Mutation | No | [2] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKLGG371 GGARDYTLRT381 FGEMADAFKS391 DYFNMPVHMV 401 PTELVEKEFW411 RLVSTIEEDV421 TVEYGADIAS431 KEFGSGFPVR441 DIKLSPEEEE 453 YLDSGWNLNN463 MPVMEQSVLA473 HITADICGMK483 LPWLYVGMCF493 SSFCWHIEDH 503 WSYSINYLHW513 GEPKTWYGVP523 GYAAEQLENV533 MKKLAPELFV543 SQPDLLHQLV 553 TIMNPNTLMT563 HEVPVYRTNQ573 CAGEFVITFP583 RAYHSGFNQG593 FNFAEAVNFC 603 TVDWLPLGRQ613 CVEHYRLLHR623 YCVFSHDEMI633 CKMASKADVL643 DVVVASTVQK 653 DMAIMIEDEK663 ALRETVRKLG673 VIDSERMDFE683 LLPDDERQCV693 KCKTTCFMSA 703 ISCSCKPGLL713 VCLHHVKELC723 SCPPYKYKLR733 YRYTLDDLYP743 MMNALKLRAE 753
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| Ligand Name: Fumaric acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human JARID1B in complex with succinate | PDB:5FY4 | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [3] |
| PDB Sequence |
SMFLPPPECP
33 VFEPSWEEFA43 DPFAFIHKIR53 PIAEQTGICK63 VRPPPDWQPP73 FACDVDKLHF 83 TPRIQRLNEL93 EAQTRVKRDY377 TLRTFGEMAD387 AFKSDYFNMP397 VHMVPTELVE 407 KEFWRLVSTI417 EEDVTVEYGA427 DIASKEFGSG437 FPVRDIKLSP449 EEEEYLDSGW 459 NLNNMPVMEQ469 SVLAHITADI479 CGMKLPWLYV489 GMCFSSFCWH499 IEDHWSYSIN 509 YLHWGEPKTW519 YGVPGYAAEQ529 LENVMKKLAP539 ELFVSQPDLL549 HQLVTIMNPN 559 TLMTHEVPVY569 RTNQCAGEFV579 ITFPRAYHSG589 FNQGFNFAEA599 VNFCTVDWLP 609 LGRQCVEHYR619 LLHRYCVFSH629 DEMICKMASK639 ADVLDVVVAS649 TVQKDMAIMI 659 EDEKALRETV669 RKLGVIDSER679 MDFELLPDDE689 RQCVKCKTTC699 FMSAISCSCK 709 PGLLVCLHHV719 KELCSCPPYK729 YKLRYRYTLD739 DLYPMMNALK749 LRAE |
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Click to View More Binding Site Information of This Target with Different Ligands | ||||||
| Different Human System Profiles of Target | Top |
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Human Similarity Proteins
of target is determined by comparing the sequence similarity of all human proteins with the target based on BLAST. The similarity proteins for a target are defined as the proteins with E-value < 0.005 and outside the protein families of the target.
A target that has fewer human similarity proteins outside its family is commonly regarded to possess a greater capacity to avoid undesired interactions and thus increase the possibility of finding successful drugs
(Brief Bioinform, 21: 649-662, 2020).
Biological Network Descriptors
of target is determined based on a human protein-protein interactions (PPI) network consisting of 9,309 proteins and 52,713 PPIs, which were with a high confidence score of ≥ 0.95 collected from STRING database.
The network properties of targets based on protein-protein interactions (PPIs) have been widely adopted for the assessment of target’s druggability. Proteins with high node degree tend to have a high impact on network function through multiple interactions, while proteins with high betweenness centrality are regarded to be central for communication in interaction networks and regulate the flow of signaling information
(Front Pharmacol, 9, 1245, 2018;
Curr Opin Struct Biol. 44:134-142, 2017).
Human Similarity Proteins
Biological Network Descriptors
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| Protein Name | Pfam ID | Percentage of Identity (%) | E value |
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| Transcription factor 19 (TCF19) | 46.939 (23/49) | 1.05E-06 |
| Degree | 4 | Degree centrality | 4.30E-04 | Betweenness centrality | 2.56E-04 |
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| Closeness centrality | 2.22E-01 | Radiality | 1.39E+01 | Clustering coefficient | 0.00E+00 |
| Neighborhood connectivity | 4.28E+01 | Topological coefficient | 2.69E-01 | Eccentricity | 11 |
| Download | Click to Download the Full PPI Network of This Target | ||||
| Chemical Structure based Activity Landscape of Target | Top |
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| Target Poor or Non Binders | Top | |||||
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| Target Poor or Non Binders | ||||||
| Target Regulators | Top | |||||
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| Target-regulating microRNAs | ||||||
| Target-interacting Proteins | ||||||
| References | Top | |||||
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| REF 1 | Identification of small molecule inhibitors of Jumonji AT-rich interactive domain 1B (JARID1B) histone demethylase by a sensitive high throughput screen. J Biol Chem. 2013 Mar 29;288(13):9408-17. | |||||
| REF 2 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Pyruvate | |||||
| REF 3 | Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Succinate | |||||
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