Structure of PDB 6p6g Chain A Binding Site BS05

Receptor Information
>6p6g 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]
PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRC
LLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSV
RLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQ
HFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSIS
LLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQ
LRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKW
EQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGT
RTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRV
THGREHSLIEDLILLLEECDANIRAS
Ligand information
Ligand IDLUP
InChIInChI=1S/C23H35F3N4O4S/c24-23(25,26)10-1-11-27-18-6-2-16(3-7-18)15-35(32,33)30-12-8-19(9-13-30)28-22(31)20-14-21(34-29-20)17-4-5-17/h14,16-19,27H,1-13,15H2,(H,28,31)/t16-,18-
InChIKeyVAYJCVQRMIULEM-SAABIXHNSA-N
SMILES
SoftwareSMILES
CACTVS 3.385FC(F)(F)CCCN[CH]1CC[CH](CC1)C[S](=O)(=O)N2CC[CH](CC2)NC(=O)c3cc(on3)C4CC4
OpenEye OEToolkits 2.0.7c1c(onc1C(=O)NC2CCN(CC2)S(=O)(=O)CC3CCC(CC3)NCCCC(F)(F)F)C4CC4
CACTVS 3.385FC(F)(F)CCCN[C@H]1CC[C@@H](CC1)C[S](=O)(=O)N2CC[C@@H](CC2)NC(=O)c3cc(on3)C4CC4
ACDLabs 12.01C4C(NCCCC(F)(F)F)CCC(CS(N1CCC(CC1)NC(=O)c3cc(C2CC2)on3)(=O)=O)C4
FormulaC23 H35 F3 N4 O4 S
Name5-cyclopropyl-N-{1-[({trans-4-[(4,4,4-trifluorobutyl)amino]cyclohexyl}methyl)sulfonyl]piperidin-4-yl}-1,2-oxazole-3-carboxamide
ChEMBLCHEMBL4460946
DrugBank
ZINC
PDB chain6p6g 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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PDB6p6g Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors.
Resolution1.59 Å
Binding residue
(original residue number in PDB)		N181 F183 C186 E192 I237 Y239 E294 V368
Binding residue
(residue number reindexed from 1)		N179 F181 C184 E190 I235 Y237 E292 V366
Annotation score1
Binding affinityMOAD: Ki=6nM
BindingDB: EC50=39nM,IC50=67nM,Ki=6.0nM
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6p6g, PDBe:6p6g, PDBj:6p6g
PDBsum6p6g
PubMed32071679
UniProtQ9H7B4|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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