Structure of PDB 5lt6 Chain A Binding Site BS04

Receptor Information
>5lt6 Chain A (length=234) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERMQCECTPLSK
DERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVIL
TEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYF
MALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLV
PSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLG
Ligand information
Ligand ID76J
InChIInChI=1S/C20H33N7O5/c1-2-3-4-7-23-11(5-6-12(21)20(30)31)8-13-15(28)16(29)19(32-13)27-10-26-14-17(22)24-9-25-18(14)27/h9-13,15-16,19,23,28-29H,2-8,21H2,1H3,(H,30,31)(H2,22,24,25)/p+2/t11-,12-,13+,15+,16+,19+/m0/s1
InChIKeyRFJREUSTWBSNNC-OAVPVUAOSA-P
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5CCCCC[NH2+][C@@H](CC[C@@H](C(=O)O)[NH3+])C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
OpenEye OEToolkits 2.0.5CCCCC[NH2+]C(CCC(C(=O)O)[NH3+])CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.385CCCCC[NH2+][C@@H](CC[C@H]([NH3+])C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
CACTVS 3.385CCCCC[NH2+][CH](CC[CH]([NH3+])C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
FormulaC20 H35 N7 O5
Name[(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium
ChEMBL
DrugBank
ZINC
PDB chain5lt6 Chain A Residue 1805 [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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PDB5lt6 Structure of the Epigenetic Oncogene MMSET and Inhibition by N-Alkyl Sinefungin Derivatives.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		K1560 G1561 W1562 Y1579 Y1605 R1625 N1628 H1629 F1664 Y1666 Q1676 C1678 F1679 L1689
Binding residue
(residue number reindexed from 1)		K104 G105 W106 Y123 Y149 R169 N172 H173 F208 Y210 Q220 C222 F223 L233
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.41,IC50=3.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y1579 Y1666
Catalytic site (residue number reindexed from 1) Y123 Y210
Enzyme Commision number 2.1.1.-
2.1.1.359: [histone H3]-lysine(36) N-trimethyltransferase.
Gene Ontology
Molecular Function
GO:0016279 protein-lysine N-methyltransferase activity
GO:0042054 histone methyltransferase activity
GO:0046975 histone H3K36 methyltransferase activity
Cellular Component
GO:0005634 nucleus

View graph for
Molecular Function
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Cellular Component
External links
PDB RCSB:5lt6, PDBe:5lt6, PDBj:5lt6
PDBsum5lt6
PubMed27571355
UniProtQ9BYW2|SETD2_HUMAN Histone-lysine N-methyltransferase SETD2 (Gene Name=SETD2)

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