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 | Pomalidomide, (S)- | Ligand Info | |||
| Canonical SMILES | C1CC(=O)NC(=O)C1N2C(=O)C3=C(C2=O)C(=CC=C3)N | ||||
| InChI | 1S/C13H11N3O4/c14-7-3-1-2-6-10(7)13(20)16(12(6)19)8-4-5-9(17)15-11(8)18/h1-3,8H,4-5,14H2,(H,15,17,18)/t8-/m0/s1 | ||||
| InChIKey | UVSMNLNDYGZFPF-QMMMGPOBSA-N | ||||
| PubChem Compound ID | 9965330 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 8D81 Cereblon~DDB1 bound to Pomalidomide | ||||||
| Method | Electron microscopy | Resolution | 3.90 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: 6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) | ||||||
| Method | X-ray diffraction | Resolution | 3.25 Å | Mutation | No | [2] |
| PDB Sequence |
GRTLHDDDSC
78 QVIPVLPQVM88 MILIPGQTLP98 LQLFHPQEVS108 MVRNLIQKDR118 TFAVLAYSNV 128 QEREAQFGTT138 AEIYAYREEQ148 DFGIEIVKVK158 AIGRQRFKVL168 ELRTQSDGIQ 178 QAKVQILPEC188 VLPSTMSAVQ198 LESLNKCQIF208 PSKPVSREDQ218 CSYKWWQKYQ 228 KRKFHCANLT238 SWPRWLYSLY248 DAETLMDRIK258 KQLREWDENL268 KDDSLPSNPI 278 DFSYRVAACL288 PIDDVLRIQL298 LKIGSAIQRL308 RCELDIMNKC318 TSLCCKQCQE 328 TEITTKNEIF338 SLSLCGPMAA348 YVNPHGYVHE358 TLTVYKACNL368 NLIGRPSTEH 378 SWFPGYAWTV388 AQCKICASHI398 GWKFTATKKD408 MSPQKFWGLT418 RSALLPTIPD 428 TEDEISPDKV438 ILCL
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| PDB ID: 6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) | ||||||
| Method | X-ray diffraction | Resolution | 4.25 Å | Mutation | No | [2] |
| 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 LLPTIPDTED431 EISPDKVILC441 L |
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| PDB ID: 6UML Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex | ||||||
| Method | X-ray diffraction | Resolution | 3.58 Å | Mutation | No | [3] |
| PDB Sequence |
NFDTSLPTSH
57 TYLFHGRTLH73 DDDSCQVIPV83 LPQVMMILIP93 GQTLPLQLFH103 PQEVSMVRNL 113 IQKDRTFAVL123 YSEAQFGTTA139 EIYAYREEQD149 FGIEIVKVKA159 IGRQRFKQAK 181 VQILPECVLP191 STMSAVQLES201 LNKCQIFSYK222 WWQKYQKRKF232 HCANLTSWPR 242 WLYSLYDAET252 LMDRIKKQLR262 EWDLPSNPID279 FSYRVAACLP289 IDDVLRIQLL 299 KIGSAIQRLR309 CELDIMNKCT319 SLCCKQCQET329 EITTKNEIFS339 LSLCGPMAAY 349 VNPHGYVHET359 LTVYKACNLN369 LIGRPSTEHS379 WFPGYAWTVA389 QCKICASHIG 399 WKFTATKKDM409 SPQKFWGLTR419 SALLPTIP
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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. | ||||
| REF 2 | Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. Science. 2018 Nov 2;362(6414):eaat0572. | ||||
| REF 3 | Crystal structure of the SALL4-pomalidomide-cereblon-DDB1 complex. Nat Struct Mol Biol. 2020 Apr;27(4):319-322. | ||||
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