Structure of PDB 7xe3 Chain A Binding Site BS05

Receptor Information
>7xe3 Chain A (length=747) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEKKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNEC
FDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKP
ECRKWRQLTKEIQLTPQIAKTYRCGMKPNTTSDHCSLPEDLRVLEVSNHW
WYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTSVPGMNRYFQPFYQP
NECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEA
LTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYL
LPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDK
SFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRIT
DPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESG
IQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLL
TPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLV
TVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKV
QGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLD
DKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGS
GEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF
Ligand information
Ligand ID8A2
InChIInChI=1S/C9H7BrF2O/c10-7-5-8(11)6(2-1-3-13)4-9(7)12/h3-5H,1-2H2
InChIKeyJXYLPBJZJRAAJO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1cc(CCC=O)c(F)cc1Br
OpenEye OEToolkits 2.0.7c1c(c(cc(c1F)Br)F)CCC=O
FormulaC9 H7 Br F2 O
Name3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal
ChEMBL
DrugBank
ZINC
PDB chain7xe3 Chain A Residue 905 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7xe3 Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2
Resolution2.82 Å
Binding residue
(original residue number in PDB)		N440 Y767 Q803 T804
Binding residue
(residue number reindexed from 1)		N365 Y692 Q728 T729
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:0003682 chromatin binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016491 oxidoreductase activity
GO:0032452 histone demethylase activity
GO:0032453 histone H3K4 demethylase activity
GO:0042393 histone binding
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
GO:0140682 FAD-dependent H3K4me/H3K4me3 demethylase activity
Biological Process
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0044726 epigenetic programing of female pronucleus
GO:0071514 genomic imprinting
Cellular Component
GO:0000786 nucleosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7xe3, PDBe:7xe3, PDBj:7xe3
PDBsum7xe3
PubMed
UniProtQ8NB78|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

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