Structure of PDB 7xw8 Chain A

Receptor sequence

>7xw8A (length=639) Species: 9606 (Homo sapiens)

SSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV
PKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHITAEFLVKSKH
RDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFA
NLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDI
KLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQP
PAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGST
TASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGI
FGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPQP
IPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLG

3D structure

• PDB: 7xw8 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.
• Chain: A
• Resolution: 2.28 Å

Enzymatic activity

• 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	FA8	A	G285 G287 S289 L307 E308 A309 R310 G315 R316 G330 A331 M332 V333 V590 L625 P626 W751 W756 S760 Y761 G800 E801 T810 V811 A814	G115 G117 S119 L137 E138 A139 R140 G145 R146 G160 A161 M162 V163 V406 L441 P442 W567 W572 S576 Y577 G608 E609 T618 V619 A622
BS02	I00	A	F538 W695 Y761 A809	F354 W511 Y577 A617

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0006355 regulation of DNA-templated transcription

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:7xw8, PDBe:7xw8, PDBj:7xw8
• PDBsum: 7xw8
• PubMed: 35749987
• UniProt: O60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)