5LHG

Structure of the KDM1A/CoREST complex with the inhibitor 4-methyl-N-[4-[[4-(1-methylpiperidin-4-yl)oxyphenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Flavoreductase-like	8017500	3000055	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LSD1 insert domain-like	8056826	3002361	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Flavoreductase-like	8017500	3000055	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Homeodomain-like	8001517	3000001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CoREST LSD1-binding region-like	8056844	3002363	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8044642	3000001	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SWIRM	e5lhgA3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: SWIRM	ECOD (1.6)
A	Amino_oxidase_2nd	e5lhgA2	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: Amino_oxidase_2nd	ECOD (1.6)
A	Amino_oxidase_1st	e5lhgA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Amino_oxidase_1st	ECOD (1.6)
B	Myb_DNA-binding_3	e5lhgB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Myb_DNA-binding_3	ECOD (1.6)
B	KOG1194	e5lhgB2	A: extended segments	X: Helical region in REST corepressor 1 (From Topology)	H: Helical region in REST corepressor 1 (From Topology)	T: Helical region in REST corepressor 1	F: KOG1194	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	1.10.287.80	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	ATP synthase, gamma subunit, helix hairpin domain	CATH (4.3.0)
B	1.20.58.1880	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04433	SWIRM domain (SWIRM)	SWIRM domain	This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA [1].	Domain
A	PF01593	Flavin containing amine oxidoreductase (Amino_oxidase)	Flavin containing amine oxidoreductase	This family consists of various amine oxidases, including maze polyamine oxidase (PAO) [1] and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene ...	This family consists of various amine oxidases, including maze polyamine oxidase (PAO) [1] and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines [2]. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium [3]. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines [1]. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins.	Domain
B	PF00249	Myb-like DNA-binding domain (Myb_DNA-binding)	Myb-like DNA-binding domain	This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1].	Domain
B	PF20878	Helical region in REST corepressor (REST_helical)	Helical region in REST corepressor	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Lysine-specific histone demethylase 1A	transcription factor binding protein binding binding bHLH transcription factor binding DNA-binding transcription factor binding MRF binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding transcription factor binding protein binding binding bHLH transcription factor binding DNA-binding transcription factor binding MRF binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding chromatin binding promoter-specific chromatin binding RNA binding telomeric repeat-containing RNA binding nucleic acid binding catalytic activity demethylase activity catalytic activity, acting on a protein protein demethylase activity histone H3 demethylase activity histone modifying activity histone demethylase activity histone H3K4 demethylase activity FAD-dependent H3K4me/H3K4me3 demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity transcription coactivator activity transcription regulator activity transcription coregulator activity nuclear receptor coactivator activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding p53 binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear androgen receptor binding histone H3K9 demethylase activity enzyme binding	nucleobase-containing compound metabolic process guanine metabolic process purine nucleobase metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process primary metabolic process purine-containing compound metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process regulation of double-strand break repair response to stimulus nucleobase-containing compound metabolic process guanine metabolic process purine nucleobase metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process primary metabolic process purine-containing compound metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress regulation of primary metabolic process cellular response to stress response to stress regulation of response to stress recombinational repair regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination DNA repair double-strand break repair regulation of biological process DNA recombination biological regulation DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination DNA damage response regulation of response to stimulus cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of protein binding regulation of molecular function negative regulation of protein binding negative regulation of binding regulation of binding negative regulation of molecular function DNA repair-dependent chromatin remodeling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis regulation of stem cell proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of biological process positive regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation positive regulation of cellular process regulation of neuron projection development multicellular organismal process regulation of cellular component organization positive regulation of cellular component organization cellular developmental process cell projection organization cell development neuron projection development neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization head development forebrain development animal organ development brain development pallium development cerebral cortex development central nervous system development telencephalon development muscle structure development muscle cell development muscle cell differentiation cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process positive regulation of neural precursor cell proliferation neural precursor cell proliferation regulation of neural precursor cell proliferation negative regulation of DNA-binding transcription factor activity regulation of DNA-binding transcription factor activity cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus response to gamma radiation regulation of epithelial to mesenchymal transition regulation of developmental process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process tissue development epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation developmental maturation anatomical structure maturation neuron maturation cell maturation signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator negative regulation of DNA damage response, signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator negative regulation of signal transduction by p53 class mediator regulation of signaling negative regulation of response to stimulus signal transduction by p53 class mediator negative regulation of signal transduction regulation of cell communication signal transduction in response to DNA damage regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process protein ubiquitination protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to nitrogen compound response to organophosphorus cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to cAMP response to organic cyclic compound homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator negative regulation of apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage negative regulation of apoptotic process intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death response to light stimulus response to UV cellular response to light stimulus cellular response to UV protein localization regulation of localization cellular localization regulation of protein localization localization regulation of cellular localization cellular macromolecule localization macromolecule localization response to antibiotic response to fungicide response to toxic substance regulation of DNA binding negative regulation of DNA binding positive regulation of cell size regulation of cellular component size regulation of biological quality regulation of cell size regulation of anatomical structure size DNA methylation-dependent heterochromatin formation regulation of heterochromatin formation regulation of chromatin organization heterochromatin formation regulation of DNA methylation-dependent heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation negative regulation of gene expression, epigenetic intracellular receptor signaling pathway response to lipid hormone-mediated signaling pathway cellular response to endogenous stimulus response to hormone response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway androgen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus regulation of androgen receptor signaling pathway cellular response to lipid nuclear receptor-mediated signaling pathway neuroblast proliferation positive regulation of nervous system development regulation of neuroblast proliferation regulation of neurogenesis regulation of cell development regulation of nervous system development positive regulation of neurogenesis regulation of multicellular organismal development positive regulation of cell development positive regulation of neuroblast proliferation protein dealkylation protein demethylation demethylation	protein-containing complex catalytic complex DNA repair complex transcription regulator complex intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle chromosome, telomeric region chromosomal region protein-containing complex catalytic complex DNA repair complex transcription regulator complex intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B	REST corepressor 1	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding protein binding enzyme binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process multicellular organismal process cellular developmental process regulation of developmental process regulation of megakaryocyte differentiation positive regulation of biological process megakaryocyte differentiation cell development regulation of cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation cell differentiation anatomical structure development regulation of immune system process regulation of multicellular organismal process positive regulation of megakaryocyte differentiation positive regulation of cellular process developmental process regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation myeloid cell differentiation immune system process positive regulation of myeloid cell differentiation regulation of hemopoiesis homeostatic process erythrocyte differentiation multicellular organismal-level homeostasis homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of gene expression cellular component organization chromatin organization cellular component organization or biogenesis	protein-containing complex catalytic complex DNA repair complex transcription regulator complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen histone deacetylase complex intracellular organelle protein-containing complex catalytic complex DNA repair complex transcription regulator complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002937	Amine oxidase	Domain
A	IPR017366	Lysine-specific histone demethylase	Family
A	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR007526	SWIRM domain	Domain
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR050281	Flavin monoamine oxidase and related enzymes	Family
B	IPR051066	Transcriptional Regulator and Corepressor	Family
B	IPR009057	Homedomain-like superfamily	Homologous Superfamily
B	IPR049048	REST corepressor, helical domain	Domain
B	IPR017884	SANT domain	Domain
B	IPR001005	SANT/Myb domain	Domain
B	IPR000949	ELM2 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O60341	palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndrome hyperplasia Neoplasm Invasiveness malignant colon neoplasm non-small cell lung carcinoma benign colon neoplasm lung cancer cancer intellectual disability colonic neoplasm large cell medulloblastoma medulloblastoma
B	Pharos: Q9UKL0	malignant colon neoplasm allergic rhinitis dermatomyositis ovarian cancer benign colon neoplasm IgA glomerulonephritis malignant glioma colonic neoplasm large cell medulloblastoma medulloblastoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.