Structure of PDB 8fj4 Chain A Binding Site BS02

Receptor Information
>8fj4 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 IDXZU
InChIInChI=1S/C20H22N2O/c23-20(22-17-8-2-1-3-9-17)15-7-4-6-14(12-15)18-13-19(18)21-16-10-5-11-16/h1-4,6-9,12,16,18-19,21H,5,10-11,13H2,(H,22,23)/t18-,19+/m1/s1
InChIKeyOGPXXRHRKMJPBF-MOPGFXCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)NC(=O)c2cccc(c2)C3CC3NC4CCC4
CACTVS 3.385O=C(Nc1ccccc1)c2cccc(c2)[C@H]3C[C@@H]3NC4CCC4
OpenEye OEToolkits 2.0.7c1ccc(cc1)NC(=O)c2cccc(c2)[C@H]3C[C@@H]3NC4CCC4
CACTVS 3.385O=C(Nc1ccccc1)c2cccc(c2)[CH]3C[CH]3NC4CCC4
ACDLabs 12.01O=C(Nc1ccccc1)c1cccc(c1)C1CC1NC1CCC1
FormulaC20 H22 N2 O
Name3-[(1R,2S)-2-(cyclobutylamino)cyclopropyl]-N-phenylbenzamide
ChEMBL
DrugBank
ZINC
PDB chain8fj4 Chain A Residue 1402 [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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PDB8fj4 Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1
Resolution2.76 Å
Binding residue
(original residue number in PDB)		N535 L536 F538 D556
Binding residue
(residue number reindexed from 1)		N365 L366 F368 D386
Annotation score1
Gene Ontology
Molecular Function
GO:0002039 p53 binding
GO:0003682 chromatin binding
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0019899 enzyme binding
GO:0030374 nuclear receptor coactivator activity
GO:0032451 demethylase activity
GO:0032452 histone demethylase activity
GO:0032453 histone H3K4 demethylase activity
GO:0032454 histone H3K9 demethylase activity
GO:0042162 telomeric DNA binding
GO:0042802 identical protein binding
GO:0043426 MRF binding
GO:0050660 flavin adenine dinucleotide binding
GO:0050681 nuclear androgen receptor binding
GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
GO:0061752 telomeric repeat-containing RNA binding
GO:0140297 DNA-binding transcription factor binding
GO:0140682 FAD-dependent H3K4me/H3K4me3 demethylase activity
GO:1990841 promoter-specific chromatin binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0002052 positive regulation of neuroblast proliferation
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006482 protein demethylation
GO:0010569 regulation of double-strand break repair via homologous recombination
GO:0010718 positive regulation of epithelial to mesenchymal transition
GO:0010976 positive regulation of neuron projection development
GO:0014070 response to organic cyclic compound
GO:0021987 cerebral cortex development
GO:0031398 positive regulation of protein ubiquitination
GO:0032091 negative regulation of protein binding
GO:0032880 regulation of protein localization
GO:0034644 cellular response to UV
GO:0036211 protein modification process
GO:0042551 neuron maturation
GO:0043392 negative regulation of DNA binding
GO:0043433 negative regulation of DNA-binding transcription factor activity
GO:0043518 negative regulation of DNA damage response, signal transduction by p53 class mediator
GO:0045793 positive regulation of cell size
GO:0045892 negative regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0046098 guanine metabolic process
GO:0055001 muscle cell development
GO:0060765 regulation of androgen receptor signaling pathway
GO:0060992 response to fungicide
GO:0071320 cellular response to cAMP
GO:0071480 cellular response to gamma radiation
GO:0090308 regulation of DNA methylation-dependent heterochromatin formation
GO:0120162 positive regulation of cold-induced thermogenesis
GO:0140861 DNA repair-dependent chromatin remodeling
GO:1902166 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:2000179 positive regulation of neural precursor cell proliferation
GO:2000648 positive regulation of stem cell proliferation
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription regulator complex
GO:0005694 chromosome
GO:0032991 protein-containing complex
GO:1990391 DNA repair complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8fj4, PDBe:8fj4, PDBj:8fj4
PDBsum8fj4
PubMed
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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