Structure of PDB 6ijl Chain A Binding Site BS01

Receptor Information
>6ijl Chain A (length=423) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRC
LLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSV
RLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQ
HFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSIS
LLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQ
LRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKW
EQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGT
RTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRV
THGREHSLIEDLILLLEECDANI
Ligand information
Ligand IDA8U
InChIInChI=1S/C28H32N4O3/c1-3-16-35-27(34)32-15-14-31(18-19(32)2)26(33)22-5-4-21-8-11-24(30-25(21)17-22)20-6-9-23(10-7-20)28(29)12-13-28/h4-11,17,19H,3,12-16,18,29H2,1-2H3/t19-/m1/s1
InChIKeyLQPPQWZUQVJLGH-LJQANCHMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCOC(=O)N1CCN(C[CH]1C)C(=O)c2ccc3ccc(nc3c2)c4ccc(cc4)C5(N)CC5
OpenEye OEToolkits 2.0.6CCCOC(=O)N1CCN(CC1C)C(=O)c2ccc3ccc(nc3c2)c4ccc(cc4)C5(CC5)N
CACTVS 3.385CCCOC(=O)N1CCN(C[C@H]1C)C(=O)c2ccc3ccc(nc3c2)c4ccc(cc4)C5(N)CC5
OpenEye OEToolkits 2.0.6CCCOC(=O)N1CCN(C[C@H]1C)C(=O)c2ccc3ccc(nc3c2)c4ccc(cc4)C5(CC5)N
FormulaC28 H32 N4 O3
Namepropyl (2~{R})-4-[2-[4-(1-azanylcyclopropyl)phenyl]quinolin-7-yl]carbonyl-2-methyl-piperazine-1-carboxylate
ChEMBL
DrugBank
ZINC
PDB chain6ijl Chain A Residue 501 [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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PDB6ijl Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3.
Resolution2.351 Å
Binding residue
(original residue number in PDB)		F183 T184 C186 M190 I214 F216 Y239 Y257 D332 V368
Binding residue
(residue number reindexed from 1)		F181 T182 C184 M188 I212 F214 Y237 Y255 D330 V366
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.93,IC50=11.7nM
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:6ijl, PDBe:6ijl, PDBj:6ijl
PDBsum6ijl
PubMed31223458
UniProtQ9H7B4|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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