Structure of PDB 6kiv Chain K Binding Site BS01

Receptor Information

>6kiv Chain K (length=179) Species: 9606 (Homo sapiens)

ARAEVHLRKSAFDMFNFLASKHRQPPELPMPMRFRHLKKTSKEAVGVYRS
PIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFR
IDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYR
GEELTYDYKFPIEKLPCNCGAKKCRKFLN

Ligand information

• Ligand ID: SAH
• InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
• InChIKey: ZJUKTBDSGOFHSH-WFMPWKQPSA-N
• SMILES:
  CACTVS 3.341: N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
  CACTVS 3.341: N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
• Formula: C14 H20 N6 O5 S
• Name: S-ADENOSYL-L-HOMOCYSTEINE
• ChEMBL: CHEMBL418052
• DrugBank: DB01752
• ZINC: ZINC000004228232
• PDB chain: 6kiv Chain K Residue 4001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6kiv Structural basis of nucleosome recognition and modification by MLL methyltransferases.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): H3839 R3841 Y3883 F3904 N3906 H3907 N3958 C3959
• Binding residue (residue number reindexed from 1): H53 R55 Y97 F118 N120 H121 N168 C169
• Annotation score: 5
• Binding affinity: BindingDB: IC50=2300nM

Enzymatic activity

• Enzyme Commision number: 2.1.1.-
  2.1.1.364: [histone H3]-lysine(4) N-methyltransferase.

External links

• PDB: RCSB:6kiv, PDBe:6kiv, PDBj:6kiv
• PDBsum: 6kiv
• PubMed: 31485071
• UniProt: Q03164|KMT2A_HUMAN Histone-lysine N-methyltransferase 2A (Gene Name=KMT2A)