Structure of PDB 4gut Chain A Binding Site BS03

Receptor Information
>4gut Chain A (length=740) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLGSRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECF
DHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPE
CRKWRQLTKEIQLTPQIAKTYRCGMKPNSDHCSLPEDLRVLEVSNHWWYS
MLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTGMNRYFQPFYQPNECGKA
LCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKC
IPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYH
NKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVT
VGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDK
RMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSEL
EGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSV
IIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLAL
LQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFF
GHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQ
QCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDI
IAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAA
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain4gut 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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PDB4gut LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation
Resolution1.998 Å
Binding residue
(original residue number in PDB)		C53 C58 H84 H90
Binding residue
(residue number reindexed from 1)		C7 C12 H38 H44
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) N440
Catalytic site (residue number reindexed from 1) N359
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:4gut, PDBe:4gut, PDBj:4gut
PDBsum4gut
PubMed23260659
UniProtQ8NB78|KDM1B_HUMAN Lysine-specific histone demethylase 2 (Gene Name=KDM1B)

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