Structure of PDB 5f2w Chain A

Receptor sequence
>5f2wA (length=341) Species: 9606 (Homo sapiens) [Search protein sequence]
NPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRAS
YDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCT
PRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILD
LVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSW
YSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFD
KVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSV
KISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
3D structure
PDB5f2w 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
ChainA
Resolution2.6 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G162 Y169 H180 E182 H268 S280
Enzyme Commision number 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.
1.14.11.69: [histone H3]-trimethyl-L-lysine(36) demethylase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ZN A H188 E190 H276 H180 E182 H268
BS02 ZN A C234 H240 C226 H232
BS03 5UP A Y132 F185 H188 E190 K206 W208 K241 H276 Y124 F177 H180 E182 K198 W200 K233 H268 PDBbind-CN: -logKd/Ki=3.98,IC50=104.2uM
BindingDB: IC50=104200nM
External links
PDB RCSB:5f2w, PDBe:5f2w, PDBj:5f2w
PDBsum5f2w
PubMed26741168
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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