Structure of PDB 6p6k Chain A

Receptor sequence

>6p6kA (length=424) Species: 9606 (Homo sapiens) [Search protein sequence]

PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRC
LLGKKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCPRYPPDSVRL
LGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHF
MREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLL
NHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLR
DQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQ
VLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRT
MEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTH
GREHSLIEDLILLLEECDANIRAS

3D structure

PDB

6p6k Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors.

Chain

Resolution

1.55 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.1.1.354: [histone H3]-lysine(4) N-trimethyltransferase.

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	C208 C261 C263 C266	C204 C257 C259 C262
BS02	ZN	A	C62 C65 H83 C87	C59 C62 H80 C84
BS03	ZN	A	C49 C52 C71 C75	C47 C50 C68 C72
BS04	SAM	A	R14 N16 Y124 E130 N132 C180 N181 S202 L203 N205 H206 Y239 Y257 F259	R12 N14 Y120 E126 N128 C176 N177 S198 L199 N201 H202 Y235 Y253 F255
BS05	L0J	A	N181 F183 T184 C186 M190 Y239 Y257 V368	N177 F179 T180 C182 M186 Y235 Y253 V364	BindingDB: IC50=1421nM

Gene Ontology

	Molecular Function
GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0000993	RNA polymerase II complex binding
GO:0001162	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding
GO:0005515	protein binding
GO:0008168	methyltransferase activity
GO:0042054	histone methyltransferase activity
GO:0046872	metal ion binding
GO:0140939	histone H4 methyltransferase activity
GO:0140954	histone H3K36 dimethyltransferase activity
GO:0140999	histone H3K4 trimethyltransferase activity

	Biological Process
GO:0006325	chromatin organization
GO:0006334	nucleosome assembly
GO:0014904	myotube cell development
GO:0032259	methylation
GO:0045184	establishment of protein localization
GO:0045944	positive regulation of transcription by RNA polymerase II
GO:0071549	cellular response to dexamethasone stimulus

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005829	cytosol

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:6p6k, PDBe:6p6k, PDBj:6p6k
PDBsum	6p6k
PubMed	32071679
UniProt	Q9H7B4\|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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