Structure of PDB 5hi7 Chain A Binding Site BS05

Receptor Information
>5hi7 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 ID62X
InChIInChI=1S/C19H32N8O5/c1-25(2)5-3-6-26(7-4-11(20)19(30)31)8-12-14(28)15(29)18(32-12)27-10-24-13-16(21)22-9-23-17(13)27/h9-12,14-15,18,28-29H,3-8,20H2,1-2H3,(H,30,31)(H2,21,22,23)/t11-,12+,14+,15+,18+/m0/s1
InChIKeyFYXRZDCUJHGULY-URQYDQELSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(C)CCCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 2.0.4CN(C)CCCN(CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
OpenEye OEToolkits 2.0.4CN(C)CCCN(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.385CN(C)CCCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01C(N(C)C)CCN(CCC(C(O)=O)N)CC1C(O)C(C(O1)n2cnc3c2ncnc3N)O
FormulaC19 H32 N8 O5
Name5'-{[(3S)-3-amino-3-carboxypropyl][3-(dimethylamino)propyl]amino}-5'-deoxyadenosine
ChEMBL
DrugBank
ZINCZINC000584905214
PDB chain5hi7 Chain A Residue 507 [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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PDB5hi7 Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		R14 N16 Y124 N132 C180 N181 F183 S202 N205 H206 Y239 Y257 F259
Binding residue
(residue number reindexed from 1)		R12 N14 Y122 N130 C178 N179 F181 S200 N203 H204 Y237 Y255 F257
Annotation score3
Binding affinityMOAD: Ki=14nM
PDBbind-CN: -logKd/Ki=7.85,Ki=14nM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5hi7, PDBe:5hi7, PDBj:5hi7
PDBsum5hi7
PubMed27066749
UniProtQ9H7B4|SMYD3_HUMAN Histone-lysine N-methyltransferase SMYD3 (Gene Name=SMYD3)

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