Structure of PDB 7o2a Chain A Binding Site BS01

Receptor Information
>7o2a Chain A (length=427) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDR
CLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDS
VRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTF
QHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSI
SLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRK
QLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWK
WEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYG
TRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMR
VTHGREHSLIEDLILLLEECDANIRAS
Ligand information
Ligand IDUZT
InChIInChI=1S/C22H31N5O3/c1-14-12-20(28)25-18-13-16(21(29)24-9-6-15-2-3-15)4-5-19(18)27(14)22(30)26-10-7-17(23)8-11-26/h4-5,13-15,17H,2-3,6-12,23H2,1H3,(H,24,29)(H,25,28)/t14-/m0/s1
InChIKeyYEYZZZLQSMITHG-AWEZNQCLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H]1CC(=O)Nc2cc(ccc2N1C(=O)N3CCC(N)CC3)C(=O)NCCC4CC4
OpenEye OEToolkits 2.0.7C[C@H]1CC(=O)Nc2cc(ccc2N1C(=O)N3CCC(CC3)N)C(=O)NCCC4CC4
CACTVS 3.385C[CH]1CC(=O)Nc2cc(ccc2N1C(=O)N3CCC(N)CC3)C(=O)NCCC4CC4
OpenEye OEToolkits 2.0.7CC1CC(=O)Nc2cc(ccc2N1C(=O)N3CCC(CC3)N)C(=O)NCCC4CC4
FormulaC22 H31 N5 O3
Name(2S)-1-(4-azanylpiperidin-1-yl)carbonyl-N-(2-cyclopropylethyl)-2-methyl-4-oxidanylidene-3,5-dihydro-2H-1,5-benzodiazepine-7-carboxamide;
(2~{S})-1-(4-azanylpiperidin-1-yl)carbonyl-~{N}-(2-cyclopropylethyl)-2-methyl-4-oxidanylidene-3,5-dihydro-2~{H}-1,5-benzodiazepine-7-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7o2a Chain A Residue 1001 [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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PDB7o2a Discovery of the SMYD3 Inhibitor BAY-6035 Using Thermal Shift Assay (TSA)-Based High-Throughput Screening.
Resolution1.57 Å
Binding residue
(original residue number in PDB)		F183 T184 C186 E192 F216 Y239 Y257 V368
Binding residue
(residue number reindexed from 1)		F182 T183 C185 E191 F215 Y238 Y256 V367
Annotation score1
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:7o2a, PDBe:7o2a, PDBj:7o2a
PDBsum7o2a
PubMed34154424
UniProtQ9H7B4|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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