7XW8: Lysine-specific histone demethylase 1A

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418 distomer, FAD-adduct. Determined by X-ray diffraction at 2.28 Å resolution. Released 12 Oct 2022.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Homo sapiens
Chains: 1
Atoms: 5,292
Mol. weight: 75.05 kDa
Ligands: MG, I00, FA8
Released: 12 Oct 2022

Explore 7XW8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XW8 contains 36 α-helices and 36 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 36 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	172-180	9
α-helix	190-195	6
α-helix	197-200	4
α-helix	204-223	20
β-strand	227	1	1
α-helix	231-237	7
α-helix	239	1
α-helix	242-244	3
α-helix	246-258	13
β-strand	268	1	1
α-helix	272-274	3
β-strand	280-284	5	2
β-strand	287	1	3
α-helix	288-299	12
β-strand	303-307	5	2
β-strand	314	1	3
β-strand	319-322	4	4
β-strand	325-328	4	4
β-strand	333-334	2	5
β-strand	338	1	6
α-helix	342-349	8
β-strand	353-355	3	5
α-helix	356-357	2
β-strand	362-363	2	7
α-helix	368	1
β-strand	369	1	7
α-helix	370-371	2
α-helix	372-394	23
β-strand	400-401	2	8
β-strand	404-405	2	8
α-helix	406	1
β-strand	407	1	9
α-helix	408-457	50
α-helix	476-485	10
α-helix	487-511	25
α-helix	515-517	3
α-helix	523-540	18
α-helix	544-546	3
β-strand	547	1	10
β-strand	548	1	9
α-helix	556-558	3
α-helix	559-560	2
β-strand	561	1	6
β-strand	565-567	3	5
α-helix	573-579	7
β-strand	583-585	3	2
β-strand	588-596	9	11
β-strand	599-606	8	11
β-strand	613-618	6	11
β-strand	620-623	4	2
α-helix	627-630	4
β-strand	638-640	3	11
α-helix	642-644	3
α-helix	645-653	9
β-strand	655-656	2	12
β-strand	660-665	6	7
β-strand	677-680	4	7
β-strand	693-695	3	7
β-strand	702-707	6	7
α-helix	710-715	6
α-helix	720-735	16
α-helix	741-743	3
β-strand	745-748	4	7
β-strand	762-763	2	12
β-strand	765	1	10
α-helix	771-777	7
α-helix	778-779	2
β-strand	780	1	2
α-helix	792-794	3
β-strand	796-798	3	2
α-helix	801-803	3
α-helix	811-830	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysine-specific histone demethylase 1A	A	protein	665	Homo sapiens	O60341 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7XW8_1 Lysine-specific histone demethylase 1A (chains A)
GGSSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQ
LTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGV
SGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQ
VNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSL
GQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEV
KPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQI
LDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNT
AVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKT
SAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVA
GEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGS
SGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQ
FLGAM

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
I00	~{N}-(oxan-4-yl)-5-(3-oxidanylidenepropyl)thiophene-3-carboxamide	C13 H17 N O3 S	1
FA8	[[(2R,3S,4S)-5-[(4AS)-7,8-dimethyl-2,4-dioxo-4A,5-dihydrobenzo[g]pteridin-10-yl…	C27 H35 N9 O15 P2	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Design, synthesis, and structure-activity relationship of TAK-418 and its derivatives as a novel series of LSD1 inhibitors with lowered risk of hematological side effects. Hattori, Y., Matsumoto, S., Morimoto, S. et al. Eur J Med Chem (2022) 239:114522-114522. DOI 10.1016/j.ejmech.2022.114522 · PubMed

Other PDB entries of the same protein (UniProt O60341 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6E1F 1.16 Å, Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1
5IT3 1.4 Å, Swirm domain of human Lsd1
5AFW 1.6 Å, Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation
7JK7 1.96 Å, Crystal structure of Importin alpha 2 in complex with LSD1 NLS S111E mutant
7JJM 2.06 Å, Crystal structure of Importin alpha 2 in complex with LSD1 NLS
2Z3Y 2.25 Å, Crystal structure of Lysine-specific demethylase1
2Z5U 2.25 Å, Crystal structure of Lysine-specific histone demethylase 1
6KGO 2.25 Å, LSD1-S2157 five-membered ring adduct model
6KGP 2.25 Å, LSD1-S2157 N5 adduct model
7E0G 2.25 Å, Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct
2DW4 2.3 Å, Crystal structure of human LSD1 at 2.3 A resolution
6KGQ 2.32 Å, LSD1-FCPA-MPE five-membered ring adduct model

Browse structure collections

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