Structure of PDB 8inl Chain A Binding Site BS02

Receptor Information
>8inl Chain A (length=648) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQL
WLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRI
KPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATF
RKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAV
PKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQE
KHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEADITAE
FLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQ
ILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVA
LAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPL
GVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNL
FGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRC
LAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMA
QPITPGPPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGA
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain8inl Chain A Residue 908 [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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PDB8inl LSD1 in complex with S2172
Resolution2.62 Å
Binding residue
(original residue number in PDB)		G285 G287 S289 L307 E308 A309 R310 G315 R316 G330 A331 M332 V333 A589 V590 L625 W751 W756 S760 Y761 G800 E801 A809 T810 V811 A814
Binding residue
(residue number reindexed from 1)		G115 G117 S119 L137 E138 A139 R140 G145 R146 G160 A161 M162 V163 A412 V413 L448 W574 W579 S583 Y584 G616 E617 A625 T626 V627 A630
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: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:8inl, PDBe:8inl, PDBj:8inl
PDBsum8inl
PubMed
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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