Structure of PDB 5vbc Chain A Binding Site BS02

Receptor Information

>5vbc Chain A (length=216) Species: 3988 (Ricinus communis)

RRLLPFVSSEDPAQRLKQMGTLASALTELQMEFSDDLTYSSGMAPRSANQ
ARFEEGGMQVLTKEDIETLEQCRAMCKRGDCPPLLVVFDSREGFTVEADG
QIKDMTFIAEYTGDVDYIRNREHDDCDSMMTLLLAKDPSKSLVICPDKRG
NIARFISGINNHTLDGKKKQNCKCVRYSVNGECRVFLVATRDIAKGERLY
YDYNGYEHEYPTQHFV

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: 5vbc Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vbc Molecular basis for the methylation specificity of ATXR5 for histone H3.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): E250 F252 D285 R312 F313 S315 G316 Y361 Y368 F373 V374
• Binding residue (residue number reindexed from 1): E92 F94 D127 R154 F155 S157 G158 Y203 Y210 F215 V216
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.1.1.369: [histone H3]-lysine(27) N-methyltransferase.

External links

• PDB: RCSB:5vbc, PDBe:5vbc, PDBj:5vbc
• PDBsum: 5vbc
• PubMed: 28383693
• UniProt: B9RU15|ATXR5_RICCO Probable Histone-lysine N-methyltransferase ATXR5 (Gene Name=ATXR5)