Structure of PDB 5vgi Chain D

Receptor sequence
>5vgiD (length=345) Species: 9606 (Homo sapiens) [Search protein sequence]
NPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRAS
YDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCT
PRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILD
LVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSW
YSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFD
KVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSC
RKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF
3D structure
PDB5vgi Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models.
ChainD
Resolution2.07 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 D C234 H240 C306 C308 C226 H232 C298 C300
BS02 9DJ D N86 Y132 F185 H188 K206 W208 H240 K241 H276 R309 N78 Y124 F177 H180 K198 W200 H232 K233 H268 R301 BindingDB: IC50=104nM
External links
PDB RCSB:5vgi, PDBe:5vgi, PDBj:5vgi
PDBsum5vgi
PubMed28835804
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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