Structure of PDB 5xxd Chain A Binding Site BS05

Receptor Information
>5xxd 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 ID8NR
InChIInChI=1S/C21H25N3O3/c1-2-27-21(26)24-11-9-23(10-12-24)20(25)17-8-7-16-13-15-5-3-4-6-18(15)22-19(16)14-17/h7-8,13-14H,2-6,9-12H2,1H3
InChIKeyYMYFCDFYTNCCDJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCOC(=O)N1CCN(CC1)C(=O)c2ccc3cc4c(nc3c2)CCCC4
CACTVS 3.385CCOC(=O)N1CCN(CC1)C(=O)c2ccc3cc4CCCCc4nc3c2
FormulaC21 H25 N3 O3
Nameethyl 4-(5,6,7,8-tetrahydroacridin-3-ylcarbonyl)piperazine-1-carboxylate
ChEMBLCHEMBL4533652
DrugBank
ZINC
PDB chain5xxd Chain A Residue 505 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5xxd Crystal structure of SmyD3 in complex with covalent inhibitor 1
Resolution2.314 Å
Binding residue
(original residue number in PDB)		N181 S182 F183 T184 C186 M190 I237 Y239 Y257
Binding residue
(residue number reindexed from 1)		N179 S180 F181 T182 C184 M188 I235 Y237 Y255
Annotation score1
Binding affinityBindingDB: IC50=>750000nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5xxd, PDBe:5xxd, PDBj:5xxd
PDBsum5xxd
PubMed
UniProtQ9H7B4|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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