Structure of PDB 5kjn Chain A Binding Site BS07

Receptor Information
>5kjn Chain A (length=429) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEY
CFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSE
TVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIA
ALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVAL
MNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRL
RDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEE
FRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQ
DWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKA
LKKAIAIMEVAHGKDHPYISEIKQEIESH
Ligand information
Ligand ID6TL
InChIInChI=1S/C33H40N6O/c40-33(35-13-7-16-37-14-5-6-15-37)28-22-27(23-34-24-28)30-9-2-4-11-32(30)39-20-18-38(19-21-39)17-12-26-25-36-31-10-3-1-8-29(26)31/h1-4,8-11,22-25,36H,5-7,12-21H2,(H,35,40)
InChIKeyVCPDGNYFXJYJFB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C(NCCCN1CCCC1)c2cncc(c2)c3ccccc3N4CCN(CC4)CCc5c[nH]c6ccccc56
OpenEye OEToolkits 2.0.5c1ccc2c(c1)c(c[nH]2)CCN3CCN(CC3)c4ccccc4c5cc(cnc5)C(=O)NCCCN6CCCC6
FormulaC33 H40 N6 O
Name5-[2-[4-[2-(1~{H}-indol-3-yl)ethyl]piperazin-1-yl]phenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)pyridine-3-carboxamide;
AZ506
ChEMBLCHEMBL4754902
DrugBank
ZINCZINC000584905217
PDB chain5kjn Chain A Residue 510 [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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PDB5kjn Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors.
Resolution2.72 Å
Binding residue
(original residue number in PDB)		K145 I149 V179 N180 N182 G183 F184 T185 Y240 S257 Y258 F259
Binding residue
(residue number reindexed from 1)		K141 I145 V175 N176 N178 G179 F180 T181 Y236 S253 Y254 F255
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.77,IC50=0.017uM
Enzymatic activity
Enzyme Commision number 2.1.1.-
2.1.1.354: [histone H3]-lysine(4) N-trimethyltransferase.
Gene Ontology
Molecular Function
GO:0000993 RNA polymerase II complex binding
GO:0002039 p53 binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0016278 lysine N-methyltransferase activity
GO:0016279 protein-lysine N-methyltransferase activity
GO:0042054 histone methyltransferase activity
GO:0046872 metal ion binding
GO:0046975 histone H3K36 methyltransferase activity
GO:0140938 histone H3 methyltransferase activity
GO:0140999 histone H3K4 trimethyltransferase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0007507 heart development
GO:0008285 negative regulation of cell population proliferation
GO:0018026 peptidyl-lysine monomethylation
GO:0018027 peptidyl-lysine dimethylation
GO:0032259 methylation
GO:0043516 regulation of DNA damage response, signal transduction by p53 class mediator
GO:1901796 regulation of signal transduction by p53 class mediator
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:5kjn, PDBe:5kjn, PDBj:5kjn
PDBsum5kjn
PubMed28002961
UniProtQ9NRG4|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

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