Structure of PDB 5lsy Chain A Binding Site BS04

Receptor Information

>5lsy Chain A (length=246) Species: 9606 (Homo sapiens)

GETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLT
RMQCECTPLEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVE
VILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIH
YYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTT
KLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRA

Ligand information

• Ligand ID: 76M
• InChI: InChI=1S/C19H31N7O5/c1-9(2)6-22-10(3-4-11(20)19(29)30)5-12-14(27)15(28)18(31-12)26-8-25-13-16(21)23-7-24-17(13)26/h7-12,14-15,18,22,27-28H,3-6,20H2,1-2H3,(H,29,30)(H2,21,23,24)/p+2/t10-,11+,12+,14+,15+,18+/m0/s1
• InChIKey: JFKLCPCUECHESR-SNDYUSLUSA-P
• SMILES:
  OpenEye OEToolkits 2.0.5: CC(C)C[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 2.0.5: CC(C)C[NH2+]C(CCC(C(=O)O)[NH3+])CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.385: CC(C)C[NH2+][CH](CC[CH]([NH3+])C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  CACTVS 3.385: CC(C)C[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
• Formula: C19 H33 N7 O5
• Name: [(2~{S},5~{R})-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]-(2-methylpropyl)azanium
• PDB chain: 5lsy Chain A Residue 1805

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5lsy Structure of the Epigenetic Oncogene MMSET and Inhibition by N-Alkyl Sinefungin Derivatives.
• Resolution: 1.62 Å
• Binding residue (original residue number in PDB): K1560 G1561 W1562 Y1579 H1603 Y1604 Y1605 R1625 F1626 M1627 N1628 H1629 F1664 Y1666 Q1669 C1678 F1679
• Binding residue (residue number reindexed from 1): K107 G108 W109 Y126 H150 Y151 Y152 R172 F173 M174 N175 H176 F211 Y213 Q216 C225 F226
• Annotation score: 2
• Binding affinity: PDBbind-CN: -logKd/Ki=6.54,IC50=0.29uM

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1579 Y1666
• Catalytic site (residue number reindexed from 1): Y126 Y213
• 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

External links

• PDB: RCSB:5lsy, PDBe:5lsy, PDBj:5lsy
• PDBsum: 5lsy
• PubMed: 27571355
• UniProt: Q9BYW2|SETD2_HUMAN Histone-lysine N-methyltransferase SETD2 (Gene Name=SETD2)