Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T27861 | Target Info | |||
| Target Name | Protein cereblon (CRBN) | ||||
| Synonyms | Protein cereblon | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | CRBN | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Mezigdomide | Ligand Info | |||
| Canonical SMILES | C1CC(=O)NC(=O)C1N2CC3=C(C2=O)C=CC=C3OCC4=CC=C(C=C4)CN5CCN(CC5)C6=C(C=C(C=C6)C#N)F | ||||
| InChI | 1S/C32H30FN5O4/c33-26-16-23(17-34)8-9-27(26)37-14-12-36(13-15-37)18-21-4-6-22(7-5-21)20-42-29-3-1-2-24-25(29)19-38(32(24)41)28-10-11-30(39)35-31(28)40/h1-9,16,28H,10-15,18-20H2,(H,35,39,40)/t28-/m0/s1 | ||||
| InChIKey | YTINZZFBHWSAGL-NDEPHWFRSA-N | ||||
| PubChem Compound ID | 137379043 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 8D7U Cereblon~DDB1 bound to CC-92480 with DDB1 in the linear conformation | ||||||
| Method | Electron microscopy | Resolution | 3.10 Å | Mutation | No | [1] |
| PDB Sequence |
KKPNIINFDT
51 SLPTSHTYLG61 ADMEEFHGRT71 LHDDDSCQVI81 PVLPQVMMIL91 IPGQTLPLQL 101 FHPQEVSMVR111 NLIQKDRTFA121 VLAYSNVQER131 EAQFGTTAEI141 YAYREEQDFG 151 IEIVKVKAIG161 RQRFKVLELR171 TQSDGIQQAK181 VQILPECVLP191 STMSAVQLES 201 LNKCQIFPSK211 PVSREDQCSY221 KWWQKYQKRK231 FHCANLTSWP241 RWLYSLYDAE 251 TLMDRIKKQL261 REWDENLKDD271 SLPSNPIDFS281 YRVAACLPID291 DVLRIQLLKI 301 GSAIQRLRCE311 LDIMNKCTSL321 CCKQCQETEI331 TTKNEIFSLS341 LCGPMAAYVN 351 PHGYVHETLT361 VYKACNLNLI371 GRPSTEHSWF381 PGYAWTVAQC391 KICASHIGWK 401 FTATKKDMSP411 QKFWGLTRSA421 LLPT
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| PDB ID: 8D7W Cereblon~DDB1 bound to CC-92480 with DDB1 in the hinged conformation | ||||||
| Method | Electron microscopy | Resolution | 3.10 Å | Mutation | No | [1] |
| PDB Sequence |
KKPNIINFDT
51 SLPTSHTYLG61 ADMEEFHGRT71 LHDDDSCQVI81 PVLPQVMMIL91 IPGQTLPLQL 101 FHPQEVSMVR111 NLIQKDRTFA121 VLAYSNVQER131 EAQFGTTAEI141 YAYREEQDFG 151 IEIVKVKAIG161 RQRFKVLELR171 TQSDGIQQAK181 VQILPECVLP191 STMSAVQLES 201 LNKCQIFPSK211 PVSREDQCSY221 KWWQKYQKRK231 FHCANLTSWP241 RWLYSLYDAE 251 TLMDRIKKQL261 REWDENLKDD271 SLPSNPIDFS281 YRVAACLPID291 DVLRIQLLKI 301 GSAIQRLRCE311 LDIMNKCTSL321 CCKQCQETEI331 TTKNEIFSLS341 LCGPMAAYVN 351 PHGYVHETLT361 VYKACNLNLI371 GRPSTEHSWF381 PGYAWTVAQC391 KICASHIGWK 401 FTATKKDMSP411 QKFWGLTRSA421 LLPT
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| PDB ID: 8D7Z Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 | ||||||
| Method | Electron microscopy | Resolution | 3.10 Å | Mutation | No | [1] |
| PDB Sequence |
NIINFDTSLP
54 TSHTYLGADM64 EEFHGRTLHD74 DDSCQVIPVL84 PQVMMILIPG94 QTLPLQLFHP 104 QEVSMVRNLI114 QKDRTFAVLA124 YSNVQEREAQ134 FGTTAEIYAY144 REEQDFGIEI 154 VKVKAIGRQR164 FKVLELRTQS174 DGIQQAKVQI184 LPECVLPSTM194 SAVQLESLNK 204 CQIFPSKPVS214 REDQCSYKWW224 QKYQKRKFHC234 ANLTSWPRWL244 YSLYDAETLM 254 DRIKKQLREW264 DENLKDDSLP274 SNPIDFSYRV284 AACLPIDDVL294 RIQLLKIGSA 304 IQRLRCELDI314 MNKCTSLCCK324 QCQETEITTK334 NEIFSLSLCG344 PMAAYVNPHG 354 YVHETLTVYK364 ACNLNLIGRP374 STEHSWFPGY384 AWTVAQCKIC394 ASHIGWKFTA 404 TKKDMSPQKF414 WGLTRSALLP424 T
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| PDB ID: 8D7V Cereblon~DDB1 bound to CC-92480 with DDB1 in the twisted conformation | ||||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | No | [1] |
| PDB Sequence |
KKPNIINFDT
51 SLPTSHTYLG61 ADMEEFHGRT71 LHDDDSCQVI81 PVLPQVMMIL91 IPGQTLPLQL 101 FHPQEVSMVR111 NLIQKDRTFA121 VLAYSNVQER131 EAQFGTTAEI141 YAYREEQDFG 151 IEIVKVKAIG161 RQRFKVLELR171 TQSDGIQQAK181 VQILPECVLP191 STMSAVQLES 201 LNKCQIFPSK211 PVSREDQCSY221 KWWQKYQKRK231 FHCANLTSWP241 RWLYSLYDAE 251 TLMDRIKKQL261 REWDENLKDD271 SLPSNPIDFS281 YRVAACLPID291 DVLRIQLLKI 301 GSAIQRLRCE311 LDIMNKCTSL321 CCKQCQETEI331 TTKNEIFSLS341 LCGPMAAYVN 351 PHGYVHETLT361 VYKACNLNLI371 GRPSTEHSWF381 PGYAWTVAQC391 KICASHIGWK 401 FTATKKDMSP411 QKFWGLTRSA421 LLPT
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .QFC or .QFC2 or .QFC3 or :3QFC;style chemicals stick;color identity;select .B:102 or .B:103 or .B:150 or .B:152 or .B:154 or .B:350 or .B:351 or .B:352 or .B:353 or .B:377 or .B:378 or .B:379 or .B:380 or .B:386 or .B:397 or .B:400 or .B:402; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Molecular glue CELMoD compounds are regulators of cereblon conformation. Science. 2022 Nov 4;378(6619):549-553. | ||||
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