Brand  (β version)

PDB ID: 6F5T

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Ligands
Code Name Style Show Link
CQK ~{N}-oxidanyl-4-(2~{H}-1,2,3,4-tetrazol-5-yl)pyridine-2-carboxamide PoSSuM
EDO 1,2-ethanediol PoSSuM
EPE 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid PoSSuM
NI Nickel (II) ion PoSSuM
SO4 Sulfate ion PoSSuM
ZN Zinc ion PoSSuM
Non-standard Residues
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Structure summary

Code : 6F5T   PDBj   RCSB PDB   PDBe
Header : OXIDOREDUCTASE
Title : Crystal Structure of KDM4D with tetrazole ligand GF057
Release Data : 2018-12-12
Compound :
mol_id molecule chains synonym
1 Lysine-specific demethylase 4D A JmjC domain-containing histone demethylation protein 3D,Jumonji domain-containing protein 2D
ec: 1.14.11.-
fragment: JMJD2D
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli BL21(DE3)  (taxid:469008)
gene: KDM4D, JHDM3D, JMJD2D
expression_system_vector_type: plasmid
Authors : Malecki, P.H., Link, A., Weiss, M.S., Heinemann, U.
Keywords : KDM4D, ligand binding, ligand optimization, drug development, tetrazole, inhibitor design, cancer, epigenetics, OXIDOREDUCTASE
Exp. method : X-RAY DIFFRACTION ( 1.5800 Å )
Citation :

Crystal Structure of KDM4D with tetrazole ligand

Malecki, P.H.,Link, A.,Weiss, M.S.  et al.
To be published 

Reaction

Chain : A
UniProt : Q6B0I6 (KDM4D_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
2 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(9)- [histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N(6)-methyl-L- lysyl(9)-[histone H3] + 2 succinate 1.14.11.66 PubMed:16603238
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