Structure of PDB 8f59 Chain A Binding Site BS02

Receptor Information
>8f59 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 IDXB6
InChIInChI=1S/C42H47N9O16P2/c1-21-14-26-27(15-22(21)2)51(31(54)13-10-23-8-11-25(12-9-23)24-6-4-3-5-7-24)33-39(47-42(59)48-40(33)58)49(26)16-28(52)34(55)29(53)17-64-68(60,61)67-69(62,63)65-18-30-35(56)36(57)41(66-30)50-20-46-32-37(43)44-19-45-38(32)50/h3-9,11-12,14-15,19-20,28-30,34-36,41,52-53,55-57H,10,13,16-18H2,1-2H3,(H,60,61)(H,62,63)(H2,43,44,45)(H2,47,48,58,59)/t28-,29+,30+,34-,35+,36+,41+/m0/s1
InChIKeyFIJOLFZARJMJRA-OPYFKSRPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1cc2c(cc1C)N(C3=C(N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C(=O)CCc7ccc(cc7)c8ccccc8
ACDLabs 12.01Cc1cc2c(cc1C)N(CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC1OC(n3cnc4c(N)ncnc43)C(O)C1O)C=1NC(=O)NC(=O)C=1N2C(=O)CCc1ccc(cc1)c1ccccc1
OpenEye OEToolkits 2.0.7Cc1cc2c(cc1C)N(C3=C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C(=O)CCc7ccc(cc7)c8ccccc8
CACTVS 3.385Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C6=C(N(C(=O)CCc7ccc(cc7)c8ccccc8)c2cc1C)C(=O)NC(=O)N6
CACTVS 3.385Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C6=C(N(C(=O)CCc7ccc(cc7)c8ccccc8)c2cc1C)C(=O)NC(=O)N6
FormulaC42 H47 N9 O16 P2
Name[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-{5-[3-([1,1'-biphenyl]-4-yl)propanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)
ChEMBL
DrugBank
ZINC
PDB chain8f59 Chain A Residue 901 [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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PDB8f59 Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1
Resolution2.8 Å
Binding residue
(original residue number in PDB)		G285 G287 S289 E308 A309 R310 G315 R316 G330 A331 M332 V333 T335 V590 L625 P626 W756 S760 Y761 G800 E801 A809 T810 V811
Binding residue
(residue number reindexed from 1)		G115 G117 S119 E138 A139 R140 G145 R146 G160 A161 M162 V163 T165 V420 L455 P456 W586 S590 Y591 G630 E631 A639 T640 V641
Annotation score1
Enzymatic activity
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: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:8f59, PDBe:8f59, PDBj:8f59
PDBsum8f59
PubMed
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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