Structure of PDB 5arg Chain A Binding Site BS04

Receptor Information
>5arg Chain A (length=426) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYC
FTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSET
VRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAA
LHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALM
NHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLR
DSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEF
RRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQD
WEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKAL
KKAIAIMEVAHGKDHPYISEIKQEIE
Ligand information
Ligand IDH41
InChIInChI=1S/C22H20Cl2F2N6O3/c1-2-31(19(34)11-33)18-10-32(30-20(18)13-6-7-16(23)17(24)8-13)22(28-12-27)29-14-4-3-5-15(9-14)35-21(25)26/h3-9,18,21,33H,2,10-11H2,1H3,(H,28,29)/t18-/m0/s1
InChIKeyOTTJIRVZJJGFTK-SFHVURJKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCN(C1CN(N=C1c2ccc(c(c2)Cl)Cl)C(=NC#N)Nc3cccc(c3)OC(F)F)C(=O)CO
OpenEye OEToolkits 1.7.6CCN([C@H]1CN(N=C1c2ccc(c(c2)Cl)Cl)/C(=N/C#N)/Nc3cccc(c3)OC(F)F)C(=O)CO
CACTVS 3.385CCN([CH]1CN(N=C1c2ccc(Cl)c(Cl)c2)C(Nc3cccc(OC(F)F)c3)=NC#N)C(=O)CO
CACTVS 3.385CCN([C@H]1CN(N=C1c2ccc(Cl)c(Cl)c2)C(Nc3cccc(OC(F)F)c3)=NC#N)C(=O)CO
FormulaC22 H20 Cl2 F2 N6 O3
NameN-[1-(N'-CYANO-N-[3-(DIFLUOROMETHOXY)PHENYL]CARBAMIMIDOYL)-3-(3,4-DICHLOROPHENYL)-4,5-DIHYDRO-1H-PYRAZOL-4-YL]-N-ETHYL-2-HYDROXYACETAMIDE
ChEMBLCHEMBL3818617
DrugBank
ZINCZINC000504786915
PDB chain5arg Chain A Residue 1432 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5arg Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (Bay-598) for the Protein Lysine Methyltransferase Smyd2.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		E104 T105 L108 N182 G183 F184 T185 S196 A203 Y217 T238 Y240 Y258
Binding residue
(residue number reindexed from 1)		E99 T100 L103 N177 G178 F179 T180 S191 A198 Y212 T233 Y235 Y253
Annotation score1
Binding affinityMOAD: ic50=27nM
PDBbind-CN: -logKd/Ki=7.57,IC50=27nM
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:5arg, PDBe:5arg, PDBj:5arg
PDBsum5arg
PubMed27075367
UniProtQ9NRG4|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

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