Structure of PDB 7xe1 Chain B Binding Site BS05

Receptor Information
>7xe1 Chain B (length=740) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFD
HYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPEC
RKWRQLTKEIQLTPQIAKTYRCGMKPSDHCSLPEDLRVLEVSNHWWYSML
ILPPLLKDSVAAPLLSAYYPDCVGMSPSCTPGMNRYFQPFYQPNECGKAL
CVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCI
PHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHN
KSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTV
GRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKR
MDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELE
GQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVI
IEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALL
QKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFG
HVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQ
CMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDII
AEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF
Ligand information
Ligand IDDIJ
InChIInChI=1S/C9H9BrO/c10-9-5-3-8(4-6-9)2-1-7-11/h3-7H,1-2H2
InChIKeyRXZJWVPNFPPSEM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(ccc1CCC=O)Br
CACTVS 3.385Brc1ccc(CCC=O)cc1
FormulaC9 H9 Br O
Name3-(4-bromophenyl)propanal
ChEMBL
DrugBank
ZINCZINC000019682858
PDB chain7xe1 Chain B Residue 905 [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]
PDB7xe1 Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2
Resolution2.07 Å
Binding residue
(original residue number in PDB)		N440 K661 T804
Binding residue
(residue number reindexed from 1)		N358 K579 T722
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7xe1, PDBe:7xe1, PDBj:7xe1
PDBsum7xe1
PubMed
UniProtQ8NB78|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

[Back to BioLiP]