UniProt Q96SW2
Protein cereblon (Q96SW2)
Protein cereblon (UniProt Q96SW2): 49 experimental structures and 1 predicted model on GenesisL1, 15 ligands bound, 189 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- Q96SW2
- Protein
- Protein cereblon
- Experimental structures
- 49
- Predicted models
- 1
- Ligands
- 15
- Pockets
- 189 · 18 records with a druggable one
Structures
50 records of Q96SW2 in the MolNFT archive: 49 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 4M91 | crystal structure of hN33/Tusc3-peptide 1 | x-ray diffraction | B | — | — |
| 4M91 | Crystal structure of HN33/TUSC3-peptide 1 | x-ray diffraction | B | — | — |
| 4TZ4 | Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide | x-ray diffraction | C | — | — |
| 4TZ4 | Crystal structure of human cereblon in complex with DDB1 and lenalidomide | x-ray diffraction | C | — | — |
| 5FQD | Structural basis of lenalidomide induced CK1A degradation by the CRL4CRBN ubiquitin ligase | x-ray diffraction | B, E | — | — |
| 5HXB | Cereblon in complex with DDB1, CC-885, and GSPT1 | x-ray diffraction | Z, C | ZN, 85C | 13 (best 0.86) |
| 5HXB | Cereblon in complex with DDB1, cc-885, and GSPT1 | x-ray diffraction | Z, C | — | — |
| 5V3O | Cereblon in complex with DDB1 and CC-220 | x-ray diffraction | C | 8W7, ZN | 12 (best 0.86) |
| 5V3O | Cereblon in complex with DDB1 and cc-220 | x-ray diffraction | C | 8W7, ZN | — |
| 6BN7 | Crystal structure of DDB1-crbn-BRD4(BD1) complex bound to DBET23 protac. | x-ray diffraction | B | ZN, RN3 | — |
| 6BN8 | Crystal structure of DDB1-crbn-BRD4(BD1) complex bound to DBET55 protac. | x-ray diffraction | B | ZN | — |
| 6BN9 | Crystal structure of DDB1-crbn-BRD4(BD1) complex bound to DBET70 protac | x-ray diffraction | B | ZN | — |
| 6BNB | Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 PROTAC | x-ray diffraction | B | ZN | — |
| 6BNB | Crystal structure of DDB1-crbn-BRD4(BD1) complex bound to DBET57 protac | x-ray diffraction | B | ZN | — |
| 6BOY | Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC. | x-ray diffraction | B | ZN, RN6 | 10 (best 0.87) |
| 6BOY | Crystal structure of DDB1-crbn-BRD4(BD1) complex bound to DBET6 protac. | x-ray diffraction | B | ZN, RN6 | — |
| 6H0F | Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) | x-ray diffraction | B, E, H, K | ZN, Y70 | — |
| 6H0F | Structure of DDB1-crbn-pomalidomide complex bound to IKZF1(ZF2) | x-ray diffraction | B, E, H, K | ZN, Y70 | — |
| 6H0G | Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) | x-ray diffraction | B, E | ZN, Y70 | — |
| 6H0G | Structure of the DDB1-crbn-pomalidomide complex bound to ZNF692(ZF4) | x-ray diffraction | B, E | ZN, Y70 | — |
| 6UML | Structural basis for thalidomide teratogenicity revealed by the cereblon-DDB1-SALL4-pomalidomide… | x-ray diffraction | C | ZN, Y70 | 12 (best 0.86) |
| 6XK9 | Cereblon in complex with DDB1, CC-90009, and GSPT1 | x-ray diffraction | Z, C | V4M, ZN | 15 (best 0.86) |
| 6XK9 | Cereblon in complex with DDB1, cc-90009, and GSPT1 | x-ray diffraction | Z, C | V4M, ZN | — |
| 7BQU | Cereblon in complex with SALL4 and (S)-thalidomide | x-ray diffraction | A | EF2, ZN | 2 (best 0.57) |
| 7BQU | Cereblon in complex with SALL4 and (S)-thalidomide | x-ray diffraction | A | EF2, ZN | — |
| 7BQV | Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide | x-ray diffraction | A | ZN, SO4 | — |
| 7LPS | Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) | x-ray diffraction | B, E, H, K | ZN, RN9 | 19 (best 0.87) |
| 7LPS | Crystal structure of DDB1-crbn-ALV1 complex bound to helios (IKZF2 ZF2) | x-ray diffraction | B, E, H, K | ZN, RN9 | — |
| 7U8F | Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 | x-ray diffraction | A, D | ZN, LWK, SO4 | 13 (best 0.86) |
| 8CVP | Cereblon-DDB1 in the Apo form | electron microscopy | B | ZN | 10 (best 0.86) |
| 8CVP | Cereblon-DDB1 in the apo form | electron microscopy | B | ZN | — |
| 8D7U | Cereblon~DDB1 bound to CC-92480 with DDB1 in the linear conformation | electron microscopy | B | ZN, QFC | 9 (best 0.86) |
| 8D7U | CEREBLON~DDB1 bound to cc-92480 with DDB1 in the linear conformation | electron microscopy | B | ZN, QFC | — |
| 8D7V | CEREBLON~DDB1 bound to cc-92480 with DDB1 in the twisted conformation | electron microscopy | B | ZN, QFC | — |
| 8D7W | CEREBLON~DDB1 bound to cc-92480 with DDB1 in the hinged conformation | electron microscopy | B | ZN, QFC | — |
| 8D7X | CEREBLON~DDB1 in the apo form with DDB1 in the hinged conformation | electron microscopy | B | ZN | — |
| 8D7Y | Cereblon-DDB1 in the apo form with DDB1 in the twisted conformation | electron microscopy | B | ZN | — |
| 8D7Z | Cereblon-DDB1 bound to cc-92480 and ikaros ZF1-2-3 | electron microscopy | B | ZN, QFC | — |
| 8D80 | Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3 | electron microscopy | B | ZN, 8W7 | — |
| 8D80 | CEREBLON~DDB1 bound to iberdomide and ikaros ZF1-2-3 | electron microscopy | B | ZN, 8W7 | — |
| 8D81 | CEREBLON~DDB1 bound to pomalidomide | electron microscopy | B | ZN, Y70 | — |
| 8DEY | Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 | x-ray diffraction | A, D | ZN, LWK | 17 (best 0.87) |
| 8OIZ | Crystal structure of human CRBN-DDB1 in complex with Pomalidomide | x-ray diffraction | B | ZN, Y70 | 12 (best 0.86) |
| 8OJH | Crystal structure of human CRBN-DDB1 in complex with compound 4 | x-ray diffraction | B | ZN, VP9 | 11 (best 0.86) |
| 8RQ1 | Crystal structure of CRBN-midi | x-ray diffraction | A | ZN | 4 (best 0.71) |
| 8RQC | Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2 | x-ray diffraction | A, D | ZN, QFC | 8 (best 0.73) |
| 8TNP | Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40 | electron microscopy | B | ZN, Y70 | 10 (best 0.86) |
| 9CUO | Crystal structure of CRBN with compound 3 | x-ray diffraction | A, B, C, D, E, F | ZN, A1A0J, SO4 | 5 (best 0.76) |
| 9GAO | Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-methylacetami… | x-ray diffraction | A, C | A1IJM, ZN | 7 (best 0.84) |
| Q96SW2 | AlphaFold monomer V2.0 prediction for protein cereblon (Q96SW2) | predicted | A | — | — |
Ligands
- ZN · Zinc ion · in 43 records
- Y70 · S-Pomalidomide · in 8 records
- QFC · Mezigdomide · in 6 records
- 8W7 · (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione · in 4 records
- SO4 · Sulfate ion · in 3 records
- EF2 · S-Thalidomide · in 2 records
- LWK · (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione · in 2 records
- RN6 · 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3, 2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl) acetamide · in 2 records
- RN9 · 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide · in 2 records
- V4M · 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide · in 2 records
- 85C · 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea · in 1 record
- A1A0J · (3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione · in 1 record
- A1IJM · 2-[4-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]phenoxy]-~{N}-methyl-ethanamide · in 1 record
- RN3 · Methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-A][1, 4]diazepin-6-yl}acetate · in 1 record
- VP9 · 4-azanyl-2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-7-methoxy-isoindole-1,3-dione · in 1 record
Experiment against prediction
- 4TZ4 chain C against the predicted model Q96SW2: TM-score 0.99, RMSD 0.67 Å
- 4TZ4 chain C against the predicted model Q96SW2: TM-score 0.99, RMSD 0.67 Å
- 8OJH chain B against the predicted model Q96SW2: TM-score 0.99, RMSD 0.70 Å
- 7LPS chain B against the predicted model Q96SW2: TM-score 0.99, RMSD 0.80 Å
- 7LPS chain B against the predicted model Q96SW2: TM-score 0.99, RMSD 0.80 Å
- 7LPS chain E against the predicted model Q96SW2: TM-score 0.99, RMSD 0.80 Å
- 7LPS chain E against the predicted model Q96SW2: TM-score 0.99, RMSD 0.80 Å
- 7LPS chain H against the predicted model Q96SW2: TM-score 0.99, RMSD 0.81 Å
- 7LPS chain H against the predicted model Q96SW2: TM-score 0.99, RMSD 0.81 Å
- 5FQD chain B against the predicted model Q96SW2: TM-score 0.99, RMSD 0.82 Å
Elsewhere
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