Structure of PDB 2w5z Chain A Binding Site BS03

Receptor Information

>2w5z Chain A (length=180) Species: 9606 (Homo sapiens)

EYNPNDEEEEEVQLKSARRATSMDLPMPMRFRHLKKTSKEAVGVYRSPIH
GRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDD
SEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEE
LTYDYKFPIEDASNKLPCNCGAKKCRKFLN

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: 2w5z Chain A Residue 4971

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2w5z Structural Basis for the Requirement of Additional Factors for Mll1 Set Domain Activity and Recognition of Epigenetic Marks.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): I3838 H3839 R3841 R3903 N3906 H3907 Y3944 C3957 N3958
• Binding residue (residue number reindexed from 1): I49 H50 R52 R114 N117 H118 Y155 C168 N169
• Annotation score: 5
• Binding affinity: BindingDB: IC50=2300nM

Enzymatic activity

• Catalytic site (original residue number in PDB): Y3858 Y3944
• Catalytic site (residue number reindexed from 1): Y69 Y155
• Enzyme Commision number: 2.1.1.-
  2.1.1.364: [histone H3]-lysine(4) N-methyltransferase.

External links

• PDB: RCSB:2w5z, PDBe:2w5z, PDBj:2w5z
• PDBsum: 2w5z
• PubMed: 19187761
• UniProt: Q03164|KMT2A_HUMAN Histone-lysine N-methyltransferase 2A (Gene Name=KMT2A)