Structure of PDB 5lgn Chain A

Receptor sequence
>5lgnA (length=670) Species: 9606 (Homo sapiens) [Search protein sequence]
PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAD
DVKVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVI
QLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEAS
EVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPP
SDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLT
VRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIY
KCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCF
DRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIME
NISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAA
GSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALL
SGLREAGRIADQFLGAMYTL
3D structure
PDB5lgn Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 1: High-Throughput Screening and Preliminary Exploration.
ChainA
Resolution3.2 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 D557 K665
Catalytic site (residue number reindexed from 1) T165 D387 K495
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 L307 E308 A309 R310 G315 R316 A331 M332 V333 V594 L629 W760 S764 Y765 G804 E805 T814 V815 A818 G115 G117 S119 L137 E138 A139 R140 G145 R146 A161 M162 V163 V424 L459 W590 S594 Y595 G634 E635 T644 V645 A648
BS02 6W0 A Q358 W699 Y765 Q188 W529 Y595 PDBbind-CN: -logKd/Ki=5.54,IC50=2.9uM
BindingDB: IC50=13400nM,Ki=43000nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5lgn, PDBe:5lgn, PDBj:5lgn
PDBsum5lgn
PubMed28186755
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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