Structure of PDB 5lsx Chain A Binding Site BS04

Receptor Information

>5lsx Chain A (length=231) Species: 9606 (Homo sapiens)

GPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTEMQCECTPLSKD
ERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILT
EKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFM
ALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVP
SGSELTFDYQFQREAQKCFCGSANCRGYLGG

Ligand information

• Ligand ID: 76O
• InChI: InChI=1S/C22H29N7O5/c23-14(22(32)33)7-6-13(25-9-12-4-2-1-3-5-12)8-15-17(30)18(31)21(34-15)29-11-28-16-19(24)26-10-27-20(16)29/h1-5,10-11,13-15,17-18,21,25,30-31H,6-9,23H2,(H,32,33)(H2,24,26,27)/p+2/t13-,14+,15-,17-,18-,21-/m1/s1
• InChIKey: FIOIMCLLFNYJFV-ZGTZEGHKSA-P
• SMILES:
  OpenEye OEToolkits 2.0.5: c1ccc(cc1)C[NH2+]C(CCC(C(=O)O)[NH3+])CC2C(C(C(O2)n3cnc4c3ncnc4N)O)O
  OpenEye OEToolkits 2.0.5: c1ccc(cc1)C[NH2+][C@H](CC[C@@H](C(=O)O)[NH3+])C[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O
  CACTVS 3.385: Nc1ncnc2n(cnc12)[CH]3O[CH](C[CH](CC[CH]([NH3+])C(O)=O)[NH2+]Cc4ccccc4)[CH](O)[CH]3O
  CACTVS 3.385: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](C[C@@H](CC[C@H]([NH3+])C(O)=O)[NH2+]Cc4ccccc4)[C@@H](O)[C@H]3O
• Formula: C22 H31 N7 O5
• Name: [(2~{R},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]-(phenylmethyl)azanium
• PDB chain: 5lsx Chain A Residue 1804

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5lsx Structure of the Epigenetic Oncogene MMSET and Inhibition by N-Alkyl Sinefungin Derivatives.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): K1560 G1561 W1562 Y1579 H1603 Y1604 Y1605 R1625 M1627 N1628 H1629 F1664 Y1666 Q1676 C1678 F1679
• Binding residue (residue number reindexed from 1): K103 G104 W105 Y122 H146 Y147 Y148 R168 M170 N171 H172 F207 Y209 Q216 C218 F219
• Annotation score: 2
• Binding affinity: PDBbind-CN: -logKd/Ki=5.92,IC50=1.2uM

Enzymatic activity

• Catalytic site (original residue number in PDB): Y1579 Y1666
• Catalytic site (residue number reindexed from 1): Y122 Y209
• 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:5lsx, PDBe:5lsx, PDBj:5lsx
• PDBsum: 5lsx
• PubMed: 27571355
• UniProt: Q9BYW2|SETD2_HUMAN Histone-lysine N-methyltransferase SETD2 (Gene Name=SETD2)