Structure of PDB 5v3h Chain A Binding Site BS02

Receptor Information
>5v3h Chain A (length=438) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KDDDDKMRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLT
VNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMV
VFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNE
KKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHL
GSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLL
YPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDM
VRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMY
QAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMG
LEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIES
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain5v3h Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5v3h Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation.
Resolution2.69 Å
Binding residue
(original residue number in PDB)		C209 C262 C264 C267
Binding residue
(residue number reindexed from 1)		C215 C268 C270 C273
Annotation score1
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:5v3h, PDBe:5v3h, PDBj:5v3h
PDBsum5v3h
PubMed29856759
UniProtQ9NRG4|SMYD2_HUMAN N-lysine methyltransferase SMYD2 (Gene Name=SMYD2)

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