Structure of PDB 5lbq Chain A Binding Site BS03

Receptor Information
>5lbq 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 ID767
InChIInChI=1S/C17H27N5O2/c1-21(2)9-7-8-18-17-19-13-11-15(24-6)14(23-5)10-12(13)16(20-17)22(3)4/h10-11H,7-9H2,1-6H3,(H,18,19,20)
InChIKeyOGNSGOBRJCYTGK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1cc2nc(NCCCN(C)C)nc(N(C)C)c2cc1OC
OpenEye OEToolkits 2.0.5CN(C)CCCNc1nc2cc(c(cc2c(n1)N(C)C)OC)OC
FormulaC17 H27 N5 O2
NameN2-(3-(dimethylamino)propyl)-6,7-dimethoxy-N4,N4-dimethylquinazoline-2,4-diamine
ChEMBL
DrugBank
ZINCZINC000584905106
PDB chain5lbq Chain A Residue 904 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5lbq Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		E559 G562
Binding residue
(residue number reindexed from 1)		E389 G392
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.11,Kd=7.78uM
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:5lbq, PDBe:5lbq, PDBj:5lbq
PDBsum5lbq
PubMed27626075
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

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