Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5LHH

Structure of the KDM1A/CoREST complex with the inhibitor 4-ethyl-N-[3-(methoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000781	cellular_component	chromosome, telomeric region
A	0000785	cellular_component	chromatin
A	0002039	molecular_function	p53 binding
A	0002052	biological_process	positive regulation of neuroblast proliferation
A	0003682	molecular_function	chromatin binding
A	0003713	molecular_function	transcription coactivator activity
A	0003714	molecular_function	transcription corepressor activity
A	0003723	molecular_function	RNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005667	cellular_component	transcription regulator complex
A	0005694	cellular_component	chromosome
A	0006325	biological_process	chromatin organization
A	0006351	biological_process	DNA-templated transcription
A	0006355	biological_process	regulation of DNA-templated transcription
A	0006357	biological_process	regulation of transcription by RNA polymerase II
A	0010569	biological_process	regulation of double-strand break repair via homologous recombination
A	0010718	biological_process	positive regulation of epithelial to mesenchymal transition
A	0016491	molecular_function	oxidoreductase activity
A	0019899	molecular_function	enzyme binding
A	0021987	biological_process	cerebral cortex development
A	0031398	biological_process	positive regulation of protein ubiquitination
A	0032452	molecular_function	histone demethylase activity
A	0032453	molecular_function	histone H3K4 demethylase activity
A	0032454	molecular_function	histone H3K9 demethylase activity
A	0032880	biological_process	regulation of protein localization
A	0032991	cellular_component	protein-containing complex
A	0034644	biological_process	cellular response to UV
A	0035097	cellular_component	histone methyltransferase complex
A	0035575	molecular_function	histone H4K20 demethylase activity
A	0040029	biological_process	epigenetic regulation of gene expression
A	0042162	molecular_function	telomeric DNA binding
A	0042551	biological_process	neuron maturation
A	0042802	molecular_function	identical protein binding
A	0043426	molecular_function	MRF binding
A	0043518	biological_process	negative regulation of DNA damage response, signal transduction by p53 class mediator
A	0045597	biological_process	positive regulation of cell differentiation
A	0045892	biological_process	negative regulation of DNA-templated transcription
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0046098	biological_process	guanine metabolic process
A	0048812	biological_process	neuron projection morphogenesis
A	0050660	molecular_function	flavin adenine dinucleotide binding
A	0050681	molecular_function	nuclear androgen receptor binding
A	0050767	biological_process	regulation of neurogenesis
A	0051240	biological_process	positive regulation of multicellular organismal process
A	0055001	biological_process	muscle cell development
A	0060765	biological_process	regulation of androgen receptor signaling pathway
A	0060992	biological_process	response to fungicide
A	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
A	0061752	molecular_function	telomeric repeat-containing RNA binding
A	0071320	biological_process	cellular response to cAMP
A	0071480	biological_process	cellular response to gamma radiation
A	0120162	biological_process	positive regulation of cold-induced thermogenesis
A	0140297	molecular_function	DNA-binding transcription factor binding
A	0140457	molecular_function	protein demethylase activity
A	0140682	molecular_function	FAD-dependent H3K4me/H3K4me3 demethylase activity
A	0140683	molecular_function	histone H3K9me/H3K9me2 demethylase activity
A	0140861	biological_process	DNA repair-dependent chromatin remodeling
A	0160217	biological_process	negative regulation of transcription initiation-coupled chromatin remodeling
A	1902166	biological_process	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
A	1902254	biological_process	negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator
A	1990391	cellular_component	DNA repair complex
A	1990841	molecular_function	promoter-specific chromatin binding
A	2000179	biological_process	positive regulation of neural precursor cell proliferation
A	2000648	biological_process	positive regulation of stem cell proliferation
B	0000118	cellular_component	histone deacetylase complex
B	0003682	molecular_function	chromatin binding
B	0003714	molecular_function	transcription corepressor activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005667	cellular_component	transcription regulator complex
B	0006325	biological_process	chromatin organization
B	0006351	biological_process	DNA-templated transcription
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0010629	biological_process	negative regulation of gene expression
B	0017053	cellular_component	transcription repressor complex
B	0019899	molecular_function	enzyme binding
B	0030218	biological_process	erythrocyte differentiation
B	0035097	cellular_component	histone methyltransferase complex
B	0045654	biological_process	positive regulation of megakaryocyte differentiation
B	0045892	biological_process	negative regulation of DNA-templated transcription
B	1990391	cellular_component	DNA repair complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	43
Details	binding site for residue FAD A 901

Chain	Residue
A	GLY285
A	GLY315
A	ARG316
A	VAL317
A	LEU329
A	GLY330
A	ALA331
A	MET332
A	VAL333
A	THR588
A	ALA589
A	GLY287
A	VAL590
A	THR624
A	LEU625
A	PRO626
A	VAL637
A	TRP751
A	TRP756
A	SER760
A	TYR761
A	GLY800
A	VAL288
A	GLU801
A	ALA809
A	THR810
A	VAL811
A	ALA814
A	6X0908
A	HOH1002
A	HOH1004
A	HOH1012
A	HOH1014
A	SER289
A	HOH1015
A	HOH1018
A	HOH1021
A	HOH1029
A	LEU307
A	GLU308
A	ALA309
A	ARG310
A	GLY314

site_id	AC2
Number of Residues	6
Details	binding site for residue GOL A 902

Chain	Residue
A	ARG310
A	ARG312
A	ARG750
A	TRP751
A	ASP754
A	GOL904

site_id	AC3
Number of Residues	10
Details	binding site for residue GOL A 903

Chain	Residue
A	VAL468
A	LYS469
A	LYS631
A	GLN652
A	ARG653
A	MET654
A	GLY655
A	PHE656
A	TYR763
A	HOH1017

site_id	AC4
Number of Residues	4
Details	binding site for residue GOL A 904

Chain	Residue
A	ARG312
A	THR319
A	LEU329
A	GOL902

site_id	AC5
Number of Residues	3
Details	binding site for residue GOL A 905

Chain	Residue
A	GLU413
A	ARG526
A	ARG688

site_id	AC6
Number of Residues	3
Details	binding site for residue GOL A 907

Chain	Residue
A	THR335
A	ASP555
A	HIS812

site_id	AC7
Number of Residues	12
Details	binding site for residue 6X0 A 908

Chain	Residue
A	VAL333
A	THR335
A	GLN358
A	PHE538
A	ALA539
A	ASP555
A	HIS564
A	TRP695
A	TYR761
A	ALA809
A	FAD901
A	HOH1021

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	99
Details	Domain: {"description":"SWIRM","evidences":[{"source":"PROSITE-ProRule","id":"PRU00247","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	121
Details	Coiled coil: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16885027","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16956976","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20164337","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21300290","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23721412","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2DW4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2H94","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HKO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2IW5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2V1D","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2X0L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2XAF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2XAG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2XAH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2XAJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2XAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2XAS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y48","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZMS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZMT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZMU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZMV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZMZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZN0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ZN1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"27292636","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25018020","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"24111946","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	51
Details	Domain: {"description":"SANT 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00624","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)