Structure of PDB 5yjo Chain A Binding Site BS04

Receptor Information
>5yjo Chain A (length=423) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRC
LLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSV
RLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQ
HFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSIS
LLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQ
LRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKW
EQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGT
RTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRV
THGREHSLIEDLILLLEECDANI
Ligand information
Ligand ID8W0
InChIInChI=1S/C24H32N4O3/c1-3-10-31-24(30)27-8-9-28(16(2)15-27)23(29)20-7-6-19-12-18-5-4-17(14-25)11-21(18)26-22(19)13-20/h6-7,12-13,16-17H,3-5,8-11,14-15,25H2,1-2H3/t16-,17+/m0/s1
InChIKeySKXOWPNKAZGYJW-DLBZAZTESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCOC(=O)N1CCN([C@H](C1)C)C(=O)c2ccc3cc4c(nc3c2)C[C@@H](CC4)CN
CACTVS 3.385CCCOC(=O)N1CCN([C@@H](C)C1)C(=O)c2ccc3cc4CC[C@@H](CN)Cc4nc3c2
OpenEye OEToolkits 2.0.6CCCOC(=O)N1CCN(C(C1)C)C(=O)c2ccc3cc4c(nc3c2)CC(CC4)CN
CACTVS 3.385CCCOC(=O)N1CCN([CH](C)C1)C(=O)c2ccc3cc4CC[CH](CN)Cc4nc3c2
FormulaC24 H32 N4 O3
Namepropyl (3~{S})-4-[[(6~{R})-6-(aminomethyl)-5,6,7,8-tetrahydroacridin-3-yl]carbonyl]-3-methyl-piperazine-1-carboxylate
ChEMBL
DrugBank
ZINC
PDB chain5yjo Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5yjo Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3.
Resolution2.135 Å
Binding residue
(original residue number in PDB)		N181 F183 T184 C186 M190 I214 F216 Y239
Binding residue
(residue number reindexed from 1)		N179 F181 T182 C184 M188 I212 F214 Y237
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.354: [histone H3]-lysine(4) N-trimethyltransferase.
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yjo, PDBe:5yjo, PDBj:5yjo
PDBsum5yjo
PubMed31223458
UniProtQ9H7B4|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

[Back to BioLiP]