2026-02-14_00000551|ligand|9YA9

Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BMS-986458 (local refined), a potent and selective BCL6 ligand directed degrader (LDD); Electron microscopy 3.09Å
Protein #1 143 residues (85% resolved)

GSLDYKDDDDKENLYFQGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE

GSLDYKDDDDKENLYFQGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE
Protein #2 467 residues (71% resolved)

MSYYHHHHHHDYDIPTTGLVPRGSMMAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

MSYYHHHHHHDYDIPTTGLVPRGSMMAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL
Non polymer #3 A1CTU

InChI=1S/C32H34ClN9O3/c1-17-16-42(32-34-15-23(33)30(38-32)36-19-5-8-25-18(12-19)13-28(44)40(25)2)11-10-24(17)35-20-4-6-21-26(14-20)41(3)39-29(21)22-7-9-27(43)37-31(22)45/h4-6,8,12,14-15,17,22,24,35H,7,9-11,13,16H2,1-3H3,(H,34,36,38)(H,37,43,45)/t17-,22-,24-/m1/s1

C[C@@H]1CN(CC[C@H]1Nc2ccc3c(c2)n(nc3[C@H]4CCC(=O)NC4=O)C)c5ncc(c(n5)Nc6ccc7c(c6)CC(=O)N7C)Cl
Non polymer #4 ZN

InChI=1S/Zn/q+2

[Zn+2]
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Reference