Structure of PDB 3pdn Chain A Binding Site BS01

Receptor Information
>3pdn 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 IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain3pdn Chain A Residue 429 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pdn Structural Insights into the Autoinhibition and Posttranslational Activation of Histone Methyltransferase SmyD3.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		R14 N16 Y124 E130 N132 N181 S202 N205 H206 Y239 Y257 F259
Binding residue
(residue number reindexed from 1)		R13 N15 Y123 E129 N131 N180 S201 N204 H205 Y238 Y256 F258
Annotation score3
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:3pdn, PDBe:3pdn, PDBj:3pdn
PDBsum3pdn
PubMed21167177
UniProtQ9H7B4|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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