Target Information
| Target General Information | Top | |||||
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| Target ID |
T16739
(Former ID: TTDI02104)
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| Target Name |
Lysine-specific histone demethylase 1 (LSD)
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| Synonyms |
Lysine-specific histone demethylase 1A; LSD1; KIAA0601; KDM1; Flavin-containing amine oxidase domain-containing protein 2; BRAF35-HDAC complex protein BHC110; AOF2
Click to Show/Hide
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| Gene Name |
KDM1A
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| Target Type |
Clinical trial target
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[1] | ||||
| Disease | [+] 9 Target-related Diseases | + | ||||
| 1 | Alzheimer disease [ICD-11: 8A20] | |||||
| 2 | Lymphoma [ICD-11: 2A80-2A86] | |||||
| 3 | Malignant haematopoietic neoplasm [ICD-11: 2B33] | |||||
| 4 | Myelodysplastic syndrome [ICD-11: 2A37] | |||||
| 5 | Acute myeloid leukaemia [ICD-11: 2A60] | |||||
| 6 | Myeloproliferative neoplasm [ICD-11: 2A20] | |||||
| 7 | Ewing sarcoma [ICD-11: 2B52] | |||||
| 8 | Lung cancer [ICD-11: 2C25] | |||||
| 9 | Solid tumour/cancer [ICD-11: 2A00-2F9Z] | |||||
| Function |
Histone demethylase that can demethylate both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7.
Click to Show/Hide
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| BioChemical Class |
CH-NH(2) donor oxidoreductase
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| UniProt ID | ||||||
| EC Number |
EC 1.-.-.-
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| Sequence |
MLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTP
RKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEY REMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGVEGAAFQ SRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEA PYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSF GMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKC PLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLV KSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFAN ATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGC EVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLN KVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISD DVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPI TPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQA TPGVPAQQSPSM Click to Show/Hide
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| 3D Structure | Click to Show 3D Structure of This Target | PDB | ||||
| HIT2.0 ID | T09DI4 | |||||
| Drugs and Modes of Action | Top | |||||
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| Clinical Trial Drug(s) | [+] 4 Clinical Trial Drugs | + | ||||
| 1 | IMG-7289 | Drug Info | Phase 2 | Acute myeloid leukaemia | [1] | |
| 2 | INCB59872 | Drug Info | Phase 1/2 | Acute myeloid leukaemia | [1] | |
| 3 | CC-90011 | Drug Info | Phase 1 | Non-hodgkin lymphoma | [1] | |
| 4 | GSK2879552 | Drug Info | Phase 1 | Small-cell lung cancer | [6] | |
| Mode of Action | [+] 1 Modes of Action | + | ||||
| Inhibitor | [+] 63 Inhibitor drugs | + | ||||
| 1 | IMG-7289 | Drug Info | [1] | |||
| 2 | INCB59872 | Drug Info | [1] | |||
| 3 | CC-90011 | Drug Info | [1] | |||
| 4 | GSK2879552 | Drug Info | [7] | |||
| 5 | Aryl cyclopropylamine derivative 3 | Drug Info | [8] | |||
| 6 | Aryl cyclopropylamine derivative 4 | Drug Info | [8] | |||
| 7 | Aryl cyclopropylamine derivative 5 | Drug Info | [8] | |||
| 8 | Benzenamine derivative 1 | Drug Info | [8] | |||
| 9 | Benzenamine derivative 2 | Drug Info | [8] | |||
| 10 | Benzenamine derivative 3 | Drug Info | [8] | |||
| 11 | Benzenamine derivative 4 | Drug Info | [8] | |||
| 12 | Cyclic peptide derivative 1 | Drug Info | [8] | |||
| 13 | Cyclopropylamine derivative 1 | Drug Info | [8] | |||
| 14 | Cyclopropylamine derivative 11 | Drug Info | [8] | |||
| 15 | Cyclopropylamine derivative 12 | Drug Info | [8] | |||
| 16 | Cyclopropylamine derivative 13 | Drug Info | [8] | |||
| 17 | Cyclopropylamine derivative 3 | Drug Info | [8] | |||
| 18 | Cyclopropylamine derivative 4 | Drug Info | [8] | |||
| 19 | Cyclopropylamine derivative 5 | Drug Info | [8] | |||
| 20 | Cyclopropylamine derivative 6 | Drug Info | [8] | |||
| 21 | Cyclopropylamine derivative 7 | Drug Info | [8] | |||
| 22 | Cyclopropylamine derivative 8 | Drug Info | [8] | |||
| 23 | Cyclopropylamine derivative 9 | Drug Info | [8] | |||
| 24 | Heteroaryl-cyclopropylamine derivative 1 | Drug Info | [8] | |||
| 25 | Heteroaryl-cyclopropylamine derivative 2 | Drug Info | [8] | |||
| 26 | Heteroaryl-cyclopropylamine derivative 3 | Drug Info | [8] | |||
| 27 | Heteroaryl-cyclopropylamine derivative 4 | Drug Info | [8] | |||
| 28 | N-(2-phenylcyclopropyl) amino acid derivative 3 | Drug Info | [8] | |||
| 29 | N6-cyclopropyllydine derivative 1 | Drug Info | [8] | |||
| 30 | PMID25399762-Compound-Table 6-10 | Drug Info | [9] | |||
| 31 | PMID25399762-Compound-Table 6-11 | Drug Info | [9] | |||
| 32 | PMID25399762-Compound-Table 6-12 | Drug Info | [9] | |||
| 33 | PMID25399762-Compound-Table 6-13 | Drug Info | [9] | |||
| 34 | PMID25399762-Compound-Table 6-14 | Drug Info | [9] | |||
| 35 | PMID25399762-Compound-Table 6-15 | Drug Info | [9] | |||
| 36 | PMID25399762-Compound-Table 6-9 | Drug Info | [9] | |||
| 37 | PMID27019002-Compound-13 | Drug Info | [8] | |||
| 38 | PMID27019002-Compound-16 | Drug Info | [8] | |||
| 39 | PMID27019002-Compound-20a | Drug Info | [8] | |||
| 40 | PMID27019002-Compound-20b | Drug Info | [8] | |||
| 41 | PMID27019002-Compound-21b | Drug Info | [8] | |||
| 42 | PMID27019002-Compound-28 | Drug Info | [8] | |||
| 43 | PMID27019002-Compound-28a | Drug Info | [8] | |||
| 44 | PMID27019002-Compound-31a | Drug Info | [8] | |||
| 45 | PMID27019002-Compound-31b | Drug Info | [8] | |||
| 46 | PMID27019002-Compound-41 | Drug Info | [8] | |||
| 47 | PMID27019002-Compound-42b | Drug Info | [8] | |||
| 48 | PMID27019002-Compound-43a | Drug Info | [8] | |||
| 49 | PMID27019002-Compound-43b | Drug Info | [8] | |||
| 50 | PMID27019002-Compound-43c | Drug Info | [8] | |||
| 51 | PMID27019002-Compound-45 | Drug Info | [8] | |||
| 52 | PMID27019002-Compound-48 | Drug Info | [8] | |||
| 53 | PMID27019002-Compound-49 | Drug Info | [8] | |||
| 54 | PMID27019002-Compound-50 | Drug Info | [8] | |||
| 55 | Pyrimidine derivative 16 | Drug Info | [8] | |||
| 56 | Pyrimidine derivative 17 | Drug Info | [8] | |||
| 57 | Pyrimidine derivative 18 | Drug Info | [8] | |||
| 58 | Tarnylcypromine derivative 1 | Drug Info | [8] | |||
| 59 | Tarnylcypromine derivative 2 | Drug Info | [8] | |||
| 60 | Tarnylcypromine derivative 3 | Drug Info | [8] | |||
| 61 | GSK-LSD1 | Drug Info | [10] | |||
| 62 | NCL-1 | Drug Info | [11] | |||
| 63 | OG-L002 | Drug Info | [12] | |||
| 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: CC-90011 | Ligand Info | |||||
| Structure Description | Crystal structure of Lysine Specific Demethylase 1 (LSD1) with CC-90011 | PDB:6W4K | ||||
| Method | X-ray diffraction | Resolution | 2.93 Å | Mutation | No | [13] |
| PDB Sequence |
VEGAAFQSRL
183 PHDRMTSQEA193 ACFPDIISGP203 QQTQKVFLFI213 RNRTLQLWLD223 NPKIQLTFEA 233 TLQQLEAPYN243 SDTVLVHRVH253 SYLERHGLIN263 FGIYKRIKPL273 PTKKTGKVII 283 IGSGVSGLAA293 ARQLQSFGMD303 VTLLEARDRV313 GGRVATFRKG323 NYVADLGAMV 333 VTGLGGNPMM351 ELAKIKQKCP361 LYEANGQAVP371 KEKDEMVEQE381 FNRLLEATSY 391 LSHQLDFNVL401 NNKPVSLGQA411 LEVVIQLQEK421 HVKDEQIEHW431 KKIVKTQEEL 441 KELLNKMVNL451 KEKIKELHQQ461 YKEASEVKPP471 RDITAEFLVK481 SKHRDLTALC 491 KEYDELAETQ501 GKLEEKLQEL511 EANPPSDVYL521 SSRDRQILDW531 HFANLEFANA 541 TPLSTLSLKH551 WDQDDDFEFT561 GSHLTVRNGY571 SCVPVALAEG581 LDIKLNTAVR 591 QVRYTASGCE601 VIAVNTRSTS611 QTFIYKCDAV621 LCTLPLGVLK631 QQPPAVQFVP 641 PLPEWKTSAV651 QRMGFGNLNK661 VVLCFDRVFW671 DPSVNLFGHV681 GSTTASRGEL 691 FLFWNLYKAP701 ILLALVAGEA711 AGIMENISDD721 VIVGRCLAIL731 KGIFGSSAVP 741 QPKETVVSRW751 RADPWARGSY761 SYVAAGSSGN771 DYDLMAQPIT781 PGPSIPGAPQ 791 PIPRLFFAGE801 HTIRNYPATV811 HGALLSGLRE821 AGRIADQFLG831 A |
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GLY330
4.307
MET332
3.345
VAL333
3.111
THR335
3.681
ILE356
3.598
GLN358
2.926
PHE538
3.584
ALA539
3.304
ASN540
4.151
TRP552
4.787
ASP555
2.883
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| Ligand Name: Cinnamic acid | Ligand Info | |||||
| Structure Description | Crystal structure of LSD1-CoREST in complex with (-)-trans-2- phenylcyclopropyl-1-amine | PDB:2XAJ | ||||
| Method | X-ray diffraction | Resolution | 3.30 Å | Mutation | No | [14] |
| PDB Sequence |
PSGVEGAAFQ
180 SRLPHDRMTS190 QEAACFPDII200 SGPQQTQKVF210 LFIRNRTLQL220 WLDNPKIQLT 230 FEATLQQLEA240 PYNSDTVLVH250 RVHSYLERHG260 LINFGIYKRI270 KPLPTKKTGK 280 VIIIGSGVSG290 LAAARQLQSF300 GMDVTLLEAR310 DRVGGRVATF320 RKGNYVADLG 330 AMVVTGLGGN340 PMAVVSKQVN350 MELAKIKQKC360 PLYEANGQAV370 PKEKDEMVEQ 380 EFNRLLEATS390 YLSHQLDFNV400 LNNKPVSLGQ410 ALEVVIQLQE420 KHVKDEQIEH 430 WKKIVKTQEE440 LKELLNKMVN450 LKEKIKELHQ460 QYKEASEVKP470 PRDITAEFLV 480 KSKHRDLTAL490 CKEYDELAET500 QGKLEEKLQE510 LEANPPSDVY520 LSSRDRQILD 530 WHFANLEFAN540 ATPLSTLSLK550 HWDQDDDFEF560 TGSHLTVRNG570 YSCVPVALAE 580 GLDIKLNTAV590 RQVRYTASGC600 EVIAVNTRST610 SQTFIYKCDA620 VLCTLPLGVL 630 KQQPPAVQFV640 PPLPEWKTSA650 VQRMGFGNLN660 KVVLCFDRVF670 WDPSVNLFGH 680 VGSTTASRGE690 LFLFWNLYKA700 PILLALVAGE710 AAGIMENISD720 DVIVGRCLAI 730 LKGIFGSSAV740 PQPKETVVSR750 WRADPWARGS760 YSYVAAGSSG770 NDYDLMAQPI 780 TPGPSIPGAP790 QPIPRLFFAG800 EHTIRNYPAT810 VHGALLSGLR820 EAGRIADQFL 830 GAMYTL
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| 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).
Human Tissue Distribution
of target is determined from a proteomics study that quantified more than 12,000 genes across 32 normal human tissues. Tissue Specificity (TS) score was used to define the enrichment of target across tissues.
The distribution of targets among different tissues or organs need to be taken into consideration when assessing the target druggability, as it is generally accepted that the wider the target distribution, the greater the concern over potential adverse effects
(Nat Rev Drug Discov, 20: 64-81, 2021).
Human Pathway Affiliation
of target is determined by the life-essential pathways provided on KEGG database. The target-affiliated pathways were defined based on the following two criteria (a) the pathways of the studied target should be life-essential for both healthy individuals and patients, and (b) the studied target should occupy an upstream position in the pathways and therefore had the ability to regulate biological function.
Targets involved in a fewer pathways have greater likelihood to be successfully developed, while those associated with more human pathways increase the chance of undesirable interferences with other human processes
(Pharmacol Rev, 58: 259-279, 2006).
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
Human Tissue Distribution
Human Pathway Affiliation
Biological Network Descriptors
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| Protein Name | Pfam ID | Percentage of Identity (%) | E value |
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| Ankycorbin (RAI14) | 32.407 (35/108) | 5.00E-03 |
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Note:
If a protein has TS (tissue specficity) scores at least in one tissue >= 2.5, this protein is called tissue-enriched (including tissue-enriched-but-not-specific and tissue-specific). In the plots, the vertical lines are at thresholds 2.5 and 4.
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| KEGG Pathway | Pathway ID | Affiliated Target | Pathway Map |
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| Thermogenesis | hsa04714 | Affiliated Target |
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| Class: Organismal Systems => Environmental adaptation | Pathway Hierarchy | ||
| Degree | 33 | Degree centrality | 3.55E-03 | Betweenness centrality | 1.82E-03 |
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| Closeness centrality | 2.44E-01 | Radiality | 1.43E+01 | Clustering coefficient | 1.21E-01 |
| Neighborhood connectivity | 3.46E+01 | Topological coefficient | 5.52E-02 | 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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| Drug Property Profile of Target | Top | |
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| (1) Molecular Weight (mw) based Drug Clustering | (2) Octanol/Water Partition Coefficient (xlogp) based Drug Clustering | |
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| (3) Hydrogen Bond Donor Count (hbonddonor) based Drug Clustering | (4) Hydrogen Bond Acceptor Count (hbondacc) based Drug Clustering | |
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| (5) Rotatable Bond Count (rotbonds) based Drug Clustering | (6) Topological Polar Surface Area (polararea) based Drug Clustering | |
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| "RO5" indicates the cutoff set by lipinski's rule of five; "D123AB" colored in GREEN denotes the no violation of any cutoff in lipinski's rule of five; "D123AB" colored in PURPLE refers to the violation of only one cutoff in lipinski's rule of five; "D123AB" colored in BLACK represents the violation of more than one cutoffs in lipinski's rule of five | ||
| 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 | ||||||
| Target Profiles in Patients | Top | |||||
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| Target Expression Profile (TEP) | ||||||
| Target Affiliated Biological Pathways | Top | |||||
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| PID Pathway | [+] 3 PID Pathways | + | ||||
| 1 | Notch signaling pathway | |||||
| 2 | Coregulation of Androgen receptor activity | |||||
| 3 | Notch-mediated HES/HEY network | |||||
| Reactome | [+] 3 Reactome Pathways | + | ||||
| 1 | HDACs deacetylate histones | |||||
| 2 | Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 | |||||
| 3 | Factors involved in megakaryocyte development and platelet production | |||||
| WikiPathways | [+] 2 WikiPathways | + | ||||
| 1 | Factors involved in megakaryocyte development and platelet production | |||||
| 2 | Androgen receptor signaling pathway | |||||
| References | Top | |||||
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| REF 1 | Clinical pipeline report, company report or official report of the Pharmaceutical Research and Manufacturers of America (PhRMA) | |||||
| REF 2 | ClinicalTrials.gov (NCT02875223) A Safety and Efficacy Study of CC-90011 in Subjects With Relapsed and/or Refractory Solid Tumors and Non-Hodgkin's Lymphomas. U.S. National Institutes of Health. | |||||
| REF 3 | ClinicalTrials.gov (NCT03867253) A Multicentre,Randomised, Double-blind, Placebo-controlled, 3-arm, 24-week Parallel-group Study to Evaluate the Safety, Tolerability and Preliminary Efficacy of ORY-2001 in Patients With Mild-moderate Alzheimer's Disease. U.S.National Institutes of Health. | |||||
| REF 4 | ClinicalTrials.gov (NCT03600649) Clinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas. U.S. National Institutes of Health. | |||||
| REF 5 | ClinicalTrials.gov (NCT04282668) A Study of TAS1440 With ATRA in Subjects With r/r AML. U.S. National Institutes of Health. | |||||
| REF 6 | ClinicalTrials.gov (NCT02034123) Investigation of GSK2879552 in Subjects With Relapsed/Refractory Small Cell Lung Carcinoma. U.S. National Institutes of Health. | |||||
| REF 7 | A DNA Hypomethylation Signature Predicts Antitumor Activity of LSD1 Inhibitors in SCLC. Cancer Cell. 2015 Jul 13;28(1):57-69. | |||||
| REF 8 | LSD1 inhibitors: a patent review (2010-2015).Expert Opin Ther Pat. 2016 May;26(5):565-80. | |||||
| REF 9 | Novel monoamine oxidase inhibitors: a patent review (2012 - 2014).Expert Opin Ther Pat. 2015 Jan;25(1):91-110. | |||||
| REF 10 | URL: http://www.guidetopharmacology.org Nucleic Acids Res. 2015 Oct 12. pii: gkv1037. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. (Target id: 2669). | |||||
| REF 11 | Synthesis and biological activity of optically active NCL-1, a lysine-specific demethylase 1 selective inhibitor. Bioorg Med Chem. 2011 Jun 15;19(12):3702-8. | |||||
| REF 12 | A novel selective LSD1/KDM1A inhibitor epigenetically blocks herpes simplex virus lytic replication and reactivation from latency. MBio. 2013 Feb 5;4(1):e00558-12. | |||||
| REF 13 | Discovery of CC-90011: A Potent and Selective Reversible Inhibitor of Lysine Specific Demethylase 1 (LSD1). J Med Chem. 2020 Dec 10;63(23):14522-14529. | |||||
| REF 14 | Biochemical, structural, and biological evaluation of tranylcypromine derivatives as inhibitors of histone demethylases LSD1 and LSD2. J Am Chem Soc. 2010 May 19;132(19):6827-33. | |||||
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