Structure of PDB 5f3c Chain D Binding Site BS01

Receptor Information

>5f3c Chain D (length=341) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWK
PRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSD
KYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLR
TILDLVEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVP
PEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQ
EAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDM
VKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEF

Ligand information

Ligand ID

InChI

InChI=1S/Zn/q+2

InChIKey

PTFCDOFLOPIGGS-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.341	[Zn++]
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Zn+2]

Formula

Name

ZINC ION

PDB chain

5f3c Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	5f3c 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Resolution	2.06 Å
Binding residue (original residue number in PDB)	H188 E190 H276
Binding residue (residue number reindexed from 1)	H176 E178 H264
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1)	G158 Y165 H176 E178 H264 S276
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.

External links

PDB	RCSB:5f3c, PDBe:5f3c, PDBj:5f3c
PDBsum	5f3c
PubMed	26741168
UniProt	O75164\|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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