Structure of PDB 5lhi Chain A

Receptor sequence

>5lhiA (length=666) Species: 9606 (Homo sapiens) [Search protein sequence]

PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV
PKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKP
PRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVY
LSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNG
YSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDA
VLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVF
WDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISD
DVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSG
NDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLR
EAGRIADQFLGAMYTL

3D structure

PDB

5lhi Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure-Activity Relationship.

Chain

Resolution

3.4 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	T335
Catalytic site (residue number reindexed from 1)	T165
Enzyme Commision number	1.14.99.66: [histone-H3]-N(6),N(6)-dimethyl-L-lysine(4) FAD-dependent demethylase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	FAD	A	G285 G287 S289 E308 A309 R310 G315 R316 G330 A331 M332 V333 A589 V590 T624 L625 P626 W756 S760 Y761 G800 E801 T810 V811	G115 G117 S119 E138 A139 R140 G145 R146 G160 A161 M162 V163 A419 V420 T454 L455 P456 W586 S590 Y591 G630 E631 T640 V641
BS02	6X5	A	V333 Q358 F538 A539 D555 H564 W695 Y761 A809	V163 Q188 F368 A369 D385 H394 W525 Y591 A639	PDBbind-CN: -logKd/Ki=8.11,IC50=7.8nM BindingDB: IC50=7.8nM

Gene Ontology

	Molecular Function
GO:0002039	p53 binding
GO:0003682	chromatin binding
GO:0003713	transcription coactivator activity
GO:0005515	protein binding
GO:0016491	oxidoreductase activity
GO:0019899	enzyme binding
GO:0030374	nuclear receptor coactivator activity
GO:0032451	demethylase activity
GO:0032452	histone demethylase activity
GO:0032453	histone H3K4 demethylase activity
GO:0032454	histone H3K9 demethylase activity
GO:0042162	telomeric DNA binding
GO:0042802	identical protein binding
GO:0043426	MRF binding
GO:0050660	flavin adenine dinucleotide binding
GO:0050681	nuclear androgen receptor binding
GO:0061629	RNA polymerase II-specific DNA-binding transcription factor binding
GO:0061752	telomeric repeat-containing RNA binding
GO:0140297	DNA-binding transcription factor binding
GO:0140682	FAD-dependent H3K4me/H3K4me3 demethylase activity
GO:1990841	promoter-specific chromatin binding

	Biological Process
GO:0000122	negative regulation of transcription by RNA polymerase II
GO:0002052	positive regulation of neuroblast proliferation
GO:0006325	chromatin organization
GO:0006338	chromatin remodeling
GO:0006355	regulation of DNA-templated transcription
GO:0006357	regulation of transcription by RNA polymerase II
GO:0006482	protein demethylation
GO:0010569	regulation of double-strand break repair via homologous recombination
GO:0010718	positive regulation of epithelial to mesenchymal transition
GO:0010976	positive regulation of neuron projection development
GO:0014070	response to organic cyclic compound
GO:0021987	cerebral cortex development
GO:0031398	positive regulation of protein ubiquitination
GO:0032091	negative regulation of protein binding
GO:0032880	regulation of protein localization
GO:0034644	cellular response to UV
GO:0036211	protein modification process
GO:0042551	neuron maturation
GO:0043392	negative regulation of DNA binding
GO:0043433	negative regulation of DNA-binding transcription factor activity
GO:0043518	negative regulation of DNA damage response, signal transduction by p53 class mediator
GO:0045793	positive regulation of cell size
GO:0045892	negative regulation of DNA-templated transcription
GO:0045944	positive regulation of transcription by RNA polymerase II
GO:0046098	guanine metabolic process
GO:0055001	muscle cell development
GO:0060765	regulation of androgen receptor signaling pathway
GO:0060992	response to fungicide
GO:0071320	cellular response to cAMP
GO:0071480	cellular response to gamma radiation
GO:0090308	regulation of DNA methylation-dependent heterochromatin formation
GO:0120162	positive regulation of cold-induced thermogenesis
GO:0140861	DNA repair-dependent chromatin remodeling
GO:1902166	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:2000179	positive regulation of neural precursor cell proliferation
GO:2000648	positive regulation of stem cell proliferation

	Cellular Component
GO:0000781	chromosome, telomeric region
GO:0000785	chromatin
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005667	transcription regulator complex
GO:0005694	chromosome
GO:0032991	protein-containing complex
GO:1990391	DNA repair complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:5lhi, PDBe:5lhi, PDBj:5lhi
PDBsum	5lhi
PubMed	28186757
UniProt	O60341\|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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