Structure of PDB 5ccl Chain A Binding Site BS05

Receptor Information
>5ccl Chain A (length=425) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRC
LLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSV
RLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQ
HFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSIS
LLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQ
LRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKW
EQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGT
RTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRV
THGREHSLIEDLILLLEECDANIRA
Ligand information
Ligand ID4ZW
InChIInChI=1S/C14H17N3O2/c18-13-8-10-7-9(1-2-12(10)17-13)14(19)16-11-3-5-15-6-4-11/h1-2,7,11,15H,3-6,8H2,(H,16,19)(H,17,18)
InChIKeySWMKOYKJOHHEQD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc2c(cc1C(=O)NC3CCNCC3)CC(=O)N2
CACTVS 3.385O=C1Cc2cc(ccc2N1)C(=O)NC3CCNCC3
FormulaC14 H17 N3 O2
Name2-oxidanylidene-N-piperidin-4-yl-1,3-dihydroindole-5-carboxamide
ChEMBLCHEMBL3798717
DrugBank
ZINCZINC000076319921
PDB chain5ccl Chain A Residue 505 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ccl Novel Oxindole Sulfonamides and Sulfamides: EPZ031686, the First Orally Bioavailable Small Molecule SMYD3 Inhibitor.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		N181 S182 F183 T184 E192 S202 Y239 Y257
Binding residue
(residue number reindexed from 1)		N179 S180 F181 T182 E190 S200 Y237 Y255
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.77,IC50=17uM
BindingDB: IC50=>10000nM
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:5ccl, PDBe:5ccl, PDBj:5ccl
PDBsum5ccl
PubMed26985287
UniProtQ9H7B4|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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