Structure of PDB 6w4k Chain A

Receptor sequence

>6w4kA (length=651) Species: 9606 (Homo sapiens)

VEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLD
NPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPL
PTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKG
NYVADLGAMVVTGLGGNPMMELAKIKQKCPLYEANGQAVPKEKDEMVEQE
FNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHW
KKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVK
SKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDW
HFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEG
LDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLK
QQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHV
GSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAIL
KGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPIT
PGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLG
A

3D structure

• PDB: 6w4k Discovery of CC-90011: A Potent and Selective Reversible Inhibitor of Lysine Specific Demethylase 1 (LSD1).
• Chain: A
• Resolution: 2.93 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	V0Y	A	M332 V333 I356 Q358 F538 A539 D555 H564 K661 W695 Y761 A809	M159 V160 I175 Q177 F357 A358 D374 H383 K480 W514 Y580 A628	BindingDB: IC50=<100nM
BS02	FAD	A	G285 G287 S289 L307 E308 A309 R310 G315 R316 G330 A331 M332 V333 A589 V590 L625 P626 W756 S760 Y761 G800 E801 T810 V811 A814	G112 G114 S116 L134 E135 A136 R137 G142 R143 G157 A158 M159 V160 A408 V409 L444 P445 W575 S579 Y580 G619 E620 T629 V630 A633

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity

External links

• PDB: RCSB:6w4k, PDBe:6w4k, PDBj:6w4k
• PDBsum: 6w4k
• PubMed: 33034194
• UniProt: O60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)