Structure of PDB 5lgn Chain A Binding Site BS02

Receptor Information
>5lgn Chain A (length=670) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAD
DVKVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVI
QLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEAS
EVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPP
SDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLT
VRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIY
KCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCF
DRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIME
NISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAA
GSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALL
SGLREAGRIADQFLGAMYTL
Ligand information
Ligand ID6W0
InChIInChI=1S/C16H16N2O2S/c1-18-13-6-7-21-15(13)9-14(18)16(19)17-12-5-3-4-11(8-12)10-20-2/h3-9H,10H2,1-2H3,(H,17,19)
InChIKeyZQZRVLFBPXQREF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COCc1cccc(NC(=O)c2cc3sccc3n2C)c1
OpenEye OEToolkits 2.0.5Cn1c2ccsc2cc1C(=O)Nc3cccc(c3)COC
FormulaC16 H16 N2 O2 S
Name~{N}-[3-(methoxymethyl)phenyl]-4-methyl-thieno[3,2-b]pyrrole-5-carboxamide
ChEMBLCHEMBL4066708
DrugBank
ZINCZINC000040786272
PDB chain5lgn Chain A Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		Q358 W699 Y765
Binding residue
(residue number reindexed from 1)		Q188 W529 Y595
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.54,IC50=2.9uM
BindingDB: IC50=13400nM,Ki=43000nM
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.
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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