Structure of PDB 2uxn Chain A Binding Site BS02

Receptor Information
>2uxn Chain A (length=664) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWL
DNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKP
LPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRK
GNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPK
EKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKH
VKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPR
DITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLS
SRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYS
CVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVL
CTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWD
PSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDV
IVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGND
YDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREA
GRIADQFLGAMYTL
Ligand information
Ligand IDFDA
InChIInChI=1S/C27H35N9O15P2/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/h3-4,8-9,14-16,19-21,26,32,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H2,33,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyYPZRHBJKEMOYQH-UYBVJOGSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2NC3=C(NC(=O)NC3=O)N(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
CACTVS 3.341Cc1cc2NC3=C(NC(=O)NC3=O)N(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
ACDLabs 10.04O=C3C=2Nc1cc(c(cc1N(C=2NC(=O)N3)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)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
FormulaC27 H35 N9 O15 P2
NameDIHYDROFLAVINE-ADENINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000095099885
PDB chain2uxn Chain A Residue 900 [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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PDB2uxn Structural Basis of Histone Demethylation by Lsd1 Revealed by Suicide Inactivation.
Resolution2.72 Å
Binding residue
(original residue number in PDB)		G285 G287 S289 L307 E308 A309 R310 G315 R316 G330 A331 M332 V333 V590 L625 W751 W756 S760 Y761 G800 E801 T810 V811 A814
Binding residue
(residue number reindexed from 1)		G113 G115 S117 L135 E136 A137 R138 G143 R144 G158 A159 M160 V161 V418 L453 W579 W584 S588 Y589 G628 E629 T638 V639 A642
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T335 D553 K661
Catalytic site (residue number reindexed from 1) T163 D381 K489
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:2uxn, PDBe:2uxn, PDBj:2uxn
PDBsum2uxn
PubMed17529991
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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