Structure of PDB 5lgu Chain A Binding Site BS02

Receptor Information
>5lgu Chain A (length=666) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV
PKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKP
PRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVY
LSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNG
YSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDA
VLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVF
WDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISD
DVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSG
NDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLR
EAGRIADQFLGAMYTL
Ligand information
Ligand ID6W1
InChIInChI=1S/C26H27N3O3S/c1-29-23-11-13-33-25(23)14-24(29)26(30)28-22-5-3-2-4-19(22)17-32-21-8-6-20(7-9-21)31-16-18-10-12-27-15-18/h2-9,11,13-14,18,27H,10,12,15-17H2,1H3,(H,28,30)/t18-/m1/s1
InChIKeyOAZVHMYGOGQYLZ-GOSISDBHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5Cn1c2ccsc2cc1C(=O)Nc3ccccc3COc4ccc(cc4)OC[C@@H]5CCNC5
CACTVS 3.385Cn1c(cc2sccc12)C(=O)Nc3ccccc3COc4ccc(OC[C@@H]5CCNC5)cc4
OpenEye OEToolkits 2.0.5Cn1c2ccsc2cc1C(=O)Nc3ccccc3COc4ccc(cc4)OCC5CCNC5
CACTVS 3.385Cn1c(cc2sccc12)C(=O)Nc3ccccc3COc4ccc(OC[CH]5CCNC5)cc4
FormulaC26 H27 N3 O3 S
Name4-methyl-~{N}-[2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide
ChEMBLCHEMBL4081995
DrugBank
ZINCZINC000584905102
PDB chain5lgu Chain A Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5lgu Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure-Activity Relationship.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		A539 D555 W695 Y761 A809
Binding residue
(residue number reindexed from 1)		A369 D385 W525 Y591 A639
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.66,IC50=0.022uM
BindingDB: IC50=22nM
Enzymatic activity
Catalytic site (original residue number in PDB) T335
Catalytic site (residue number reindexed from 1) T165
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:5lgu, PDBe:5lgu, PDBj:5lgu
PDBsum5lgu
PubMed28186757
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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