Structure of PDB 3s7b Chain A Binding Site BS06

Receptor Information
>3s7b 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 IDNH5
InChIInChI=1S/C29H38Cl2N4O4/c30-23-8-6-20(18-24(23)31)10-13-32-15-12-27(38)35(22-4-2-1-3-5-22)17-16-33-14-11-21-7-9-25(36)28-29(21)39-19-26(37)34-28/h6-9,18,22,32-33,36H,1-5,10-17,19H2,(H,34,37)
InChIKeyLIBVHXXKHSODII-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1cc(c(cc1CCNCCC(=O)N(CCNCCc2ccc(c3c2OCC(=O)N3)O)C4CCCCC4)Cl)Cl
CACTVS 3.370Oc1ccc(CCNCCN(C2CCCCC2)C(=O)CCNCCc3ccc(Cl)c(Cl)c3)c4OCC(=O)Nc14
ACDLabs 12.01Clc1ccc(cc1Cl)CCNCCC(=O)N(C2CCCCC2)CCNCCc3ccc(O)c4NC(=O)COc34
FormulaC29 H38 Cl2 N4 O4
NameN-cyclohexyl-N~3~-[2-(3,4-dichlorophenyl)ethyl]-N-(2-{[2-(5-hydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-8-yl)ethyl]amino}ethyl)-beta-alaninamide
ChEMBLCHEMBL2169920
DrugBank
ZINCZINC000072316825
PDB chain3s7b Chain A Residue 439 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3s7b Structural Basis of Substrate Methylation and Inhibition of SMYD2.
Resolution2.42 Å
Binding residue
(original residue number in PDB)		K145 I149 N180 N182 G183 F184 T185 A203 T238 Y240 S257 Y258
Binding residue
(residue number reindexed from 1)		K141 I145 N176 N178 G179 F180 T181 A199 T234 Y236 S253 Y254
Annotation score1
Binding affinityMOAD: Kd=0.5uM
PDBbind-CN: -logKd/Ki=6.30,Kd=0.5uM
BindingDB: IC50=120nM,Kd=500nM,Ki=300nM
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:3s7b, PDBe:3s7b, PDBj:3s7b
PDBsum3s7b
PubMed21782458
UniProtQ9NRG4|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

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