Structure of PDB 5l3e Chain A Binding Site BS03

Receptor Information
>5l3e 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 IDE11
InChIInChI=1S/C27H38N6O2/c1-32(2)14-8-13-28-27-30-23-18-25(35-4)24(34-3)17-22(23)26(31-27)29-21-11-15-33(16-12-21)19-20-9-6-5-7-10-20/h5-7,9-10,17-18,21H,8,11-16,19H2,1-4H3,(H2,28,29,30,31)
InChIKeyYYFDMPHIONBOKZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CN(C)CCCNc1nc2cc(c(cc2c(n1)NC3CCN(CC3)Cc4ccccc4)OC)OC
ACDLabs 12.01O(c4cc1c(nc(nc1NC3CCN(Cc2ccccc2)CC3)NCCCN(C)C)cc4OC)C
CACTVS 3.370COc1cc2nc(NCCCN(C)C)nc(NC3CCN(CC3)Cc4ccccc4)c2cc1OC
FormulaC27 H38 N6 O2
NameN~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine
ChEMBLCHEMBL1232432
DrugBank
ZINCZINC000058631426
PDB chain5l3e Chain A Residue 903 [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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PDB5l3e Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		N383 E387 S390 D556 E559
Binding residue
(residue number reindexed from 1)		N213 E217 S220 D386 E389
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.18,Kd=660nM
BindingDB: Kd=243nM
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:5l3e, PDBe:5l3e, PDBj:5l3e
PDBsum5l3e
PubMed27626075
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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