Structure of PDB 5l3e Chain A Binding Site BS02

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 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5l3e Polymyxins and quinazolines are LSD1/KDM1A inhibitors with unusual structural features.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		L386 N535 L536 A539 W552 H564 W695
Binding residue
(residue number reindexed from 1)		L216 N365 L366 A369 W382 H394 W525
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5l3e, PDBe:5l3e, PDBj:5l3e
PDBsum5l3e
PubMed27626075
UniProtO60341|KDM1A_HUMAN Lysine-specific histone demethylase 1A (Gene Name=KDM1A)

[Back to BioLiP]