2026-07-25_00000248|ligand|9T9D

Crystal structure of PM54 bound to 10-mer duplex DNA; X-ray diffraction 2.10Å

DNA #1 10 bases

Raw Sequence ...

(DA)(DG)(DA)(DG)(DG)(DC)(DC)(DT)(DC)(DT)

Canonical Sequence ...

AGAGGCCTCT

Non polymer #2 A1JUN

InChI=1S/C41H43N3O11S/c1-17-10-20-11-24-39(48)44-25-14-51-40(49)41(38-23(12-21(13-45)42-41)22-8-6-7-9-26(22)55-38)15-56-37(31(44)30(43(24)4)27(20)32(47)33(17)50-5)29-28(25)36-35(52-16-53-36)18(2)34(29)54-19(3)46/h6-10,21,24-25,30-31,37,39,42,45,47-48H,11-16H2,1-5H3/t21-,24+,25+,30-,31-,37-,39?,41-/m1/s1

InChI=1S/C41H43N3O11S/c1-17-10-20-11-24-39(48)44-25-14-51-40(49)41(38-23(12-21(13-45)42-41)22-8-6-7-9-26(22)55-38)15-56-37(31(44)30(43(24)4)27(20)32(47)33(17)50-5)29-28(25)36-35(52-16-53-36)18(2)34(29)54-19(3)46/h6-10,21,24-25,30-31,37,39,42,45,47-48H,11-16H2,1-5H3/t21-,24+,25+,30-,31-,37-,39?,41-/m1/s1

SMILES: Cc1cc2c(c(c1OC)O)[C@@H]3[C@@H]4[C@H]5c6c(c7c(c(c6OC(=O)C)C)OCO7)[C@@H](N4C([C@H](C2)N3C)O)COC(=O)[C@@]8(CS5)c9c(c1ccccc1o9)C[C@@H](N8)CO

Cc1cc2c(c(c1OC)O)[C@@H]3[C@@H]4[C@H]5c6c(c7c(c(c6OC(=O)C)C)OCO7)[C@@H](N4C([C@H](C2)N3C)O)COC(=O)[C@@]8(CS5)c9c(c1ccccc1o9)C[C@@H](N8)CO

Biounit #1 homo-dimer

Biounit #2 homo-dimer

Reference