Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T42048 | Target Info | |||
| Target Name | Bromodomain-containing protein 3 (BRD3) | ||||
| Synonyms | RING3like protein; RING3L; RING3-like protein; KIAA0043 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | BRD3 | ||||
| Biochemical Class | Bromodomain | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: BI 2536 | Ligand Info | |||||
| Structure Description | Crystal structure of the second bromodomain (BD2) of human BRD3 bound to BI2536 | PDB:7L9L | ||||
| Method | X-ray diffraction | Resolution | 1.55 Å | Mutation | No | [1] |
| PDB Sequence |
SMGKLSEHLR
313 YCDSILREML323 SKKHAAYAWP333 FYKPVDAEAL343 ELHDYHDIIK353 HPMDLSTVKR 363 KMDGREYPDA373 QGFAADVRLM383 FSNCYKYNPP393 DHEVVAMARK403 LQDVFEMRFA 413 KMP
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| Ligand Name: Ro5203280 | Ligand Info | |||||
| Structure Description | Crystal structure of the second bromodomain (BD2) of human BRD3 bound to Ro3280 | PDB:7L72 | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [1] |
| PDB Sequence |
SMGKLSEHLR
313 YCDSILREML323 SKKHAAYAWP333 FYKPVDAEAL343 ELHDYHDIIK353 HPMDLSTVKR 363 KMDGREYPDA373 QGFAADVRLM383 FSNCYKYNPP393 DHEVVAMARK403 LQDVFEMRFA 413 KMP
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| Ligand Name: Bromosporine | Ligand Info | |||||
| Structure Description | Crystal structure of the second bromodomain (BD2) of human BRD3 bound to bromosporine | PDB:7LB4 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
SEHLRYCDSI
318 LREMLSKKHA328 AYAWPFYKPV338 DAEALELHDY348 HDIIKHPMDL358 STVKRKMDGR 368 EYPDAQGFAA378 DVRLMFSNCY388 KYNPPDHEVV398 AMARKLQDVF408 EMRFAKMP |
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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 .BMF or .BMF2 or .BMF3 or :3BMF;style chemicals stick;color identity;select .A:332 or .A:333 or .A:334 or .A:336 or .A:337 or .A:338 or .A:339 or .A:343 or .A:345 or .A:348 or .A:387 or .A:390 or .A:391 or .A:392 or .A:395 or .A:397; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-bromo-1H-indazol-5-amine | Ligand Info | |||||
| Structure Description | Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with 3-bromo-1H-indazol-5-amine | PDB:6QJU | ||||
| Method | X-ray diffraction | Resolution | 1.20 Å | Mutation | No | [2] |
| PDB Sequence |
RKTNQLQYMQ
43 NVVVKTLWKH53 QFAWPFYQPV63 DAIKLNLPDY73 HKIIKNPMDM83 GTIKKRLENN 93 YYWSASECMQ103 DFNTMFTNCY113 IYNKPTDDIV123 LMAQALEKIF133 LQKVAQMPQE 143 E
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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 .J58 or .J582 or .J583 or :3J58;style chemicals stick;color identity;select .A:58 or .A:59 or .A:63 or .A:68 or .A:70 or .A:73 or .A:108 or .A:111 or .A:112 or .A:115 or .A:116 or .A:122; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[[4-[[3-(~{tert}-Butylsulfonylamino)-4-Chloranyl-Phenyl]amino]-5-Methyl-Pyrimidin-2-Yl]amino]-2-Fluoranyl-~{n}-(1-Methylpiperidin-4-Yl)benzamide | Ligand Info | |||||
| Structure Description | Crystal structure of the first bromodomain (BD1) of human BRD3 bound to SG3-179 | PDB:7LAY | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [1] |
| PDB Sequence |
SMPEVSNPSK
31 PGRKTNQLQY41 MQNVVVKTLW51 KHQFAWPFYQ61 PVDAIKLNLP71 DYHKIIKNPM 81 DMGTIKKRLE91 NNYYWSASEC101 MQDFNTMFTN111 CYIYNKPTDD121 IVLMAQALEK 131 IFLQKVAQMP141 Q
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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 .5W2 or .5W22 or .5W23 or :35W2;style chemicals stick;color identity;select .A:57 or .A:58 or .A:59 or .A:63 or .A:68 or .A:70 or .A:73 or .A:112 or .A:115 or .A:116 or .A:120 or .A:121 or .A:122 or .A:125; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 11-Cyclopentyl-2-[2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]anilino]-5-methylpyrimido[4,5-b][1,4]benzodiazepin-6-one | Ligand Info | |||||
| Structure Description | Crystal structure of the first bromodomain (BD1) of human BRD3 bound to ERK5-IN-1 | PDB:7LAZ | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
EVSNPSKPGR
34 KTNQLQYMQN44 VVVKTLWKHQ54 FAWPFYQPVD64 AIKLNLPDYH74 KIIKNPMDMG 84 TIKKRLENNY94 YWSASECMQD104 FNTMFTNCYI114 YNKPTDDIVL124 MAQALEKIFL 134 QKVAQMPQ
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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 .VYJ or .VYJ2 or .VYJ3 or :3VYJ;style chemicals stick;color identity;select .A:57 or .A:58 or .A:59 or .A:61 or .A:63 or .A:67 or .A:68 or .A:70 or .A:73 or .A:112 or .A:115 or .A:116 or .A:121 or .A:122 or .A:125; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Physachenolide C | Ligand Info | |||||
| Structure Description | Physachenolide C with Bromodomain (BRD3-BD1) | PDB:7R8R | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [3] |
| PDB Sequence |
KPGRKTNQLQ
40 YMQNVVVKTL50 WKHQFAWPFY60 QPVDAIKLNL70 PDYHKIIKNP80 MDMGTIKKRL 90 ENNYYWSASE100 CMQDFNTMFT110 NCYIYNKPTD120 DIVLMAQALE130 KIFLQKVAQM 140 PQEE
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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 .8L6 or .8L62 or .8L63 or :38L6;style chemicals stick;color identity;select .A:57 or .A:58 or .A:59 or .A:63 or .A:68 or .A:70 or .A:73 or .A:111 or .A:112 or .A:115 or .A:116 or .A:121 or .A:122 or .A:125; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: tert-butyl 2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-8,11,12-triaza-1-azoniatricyclo[8.3.0.02,6]trideca-1(13),2(6),4,7,10-pentaen-9-yl]acetate | Ligand Info | |||||
| Structure Description | Crystal Structure of the second bromodomain of human BRD3 in complex with the inhibitor JQ1 | PDB:3S92 | ||||
| Method | X-ray diffraction | Resolution | 1.36 Å | Mutation | No | [4] |
| PDB Sequence |
KLSEHLRYCD
316 SILREMLSKK326 HAAYAWPFYK336 PVDAEALELH346 DYHDIIKHPM356 DLSTVKRKMD 366 GREYPDAQGF376 AADVRLMFSN386 CYKYNPPDHE396 VVAMARKLQD406 VFEMRFAKMP 416
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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 .JQ1 or .JQ12 or .JQ13 or :3JQ1;style chemicals stick;color identity;select .A:332 or .A:333 or .A:334 or .A:338 or .A:343 or .A:345 or .A:348 or .A:387 or .A:390 or .A:391 or .A:395 or .A:396 or .A:397 or .A:400; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Hexamethylene bisacetamide | Ligand Info | |||||
| Structure Description | Crystal structure of the second bromodomain of human BRD3 in complex with compound | PDB:5A7C | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [5] |
| PDB Sequence |
MGKLSEHLRY
314 CDSILREMLS324 KKHAAYAWPF334 YKPVDAEALE344 LHDYHDIIKH354 PMDLSTVKRK 364 MDGREYPDAQ374 GFAADVRLMF384 SNCYKYNPPD394 HEVVAMARKL404 QDVFEMRFAK 414 MP
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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 .5D4 or .5D42 or .5D43 or :35D4;style chemicals stick;color identity;select .A:332 or .A:333 or .A:334 or .A:338 or .A:343 or .A:345 or .A:348 or .A:387 or .A:391 or .A:395 or .A:397; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors. J Med Chem. 2021 Nov 11;64(21):15772-15786. | ||||
| REF 2 | Br-O-modomain (BRD3) halogen binding to a small molecule | ||||
| REF 3 | Physachenolide C is a Potent, Selective BET Inhibitor. J Med Chem. 2023 Jan 12;66(1):913-933. | ||||
| REF 4 | Crystal Structure of the second bromodomain of human BRD3 in complex with the inhibitor JQ1 | ||||
| REF 5 | Cancer Differentiating Agent Hexamethylene Bisacetamide Inhibits BET Bromodomain Proteins. Cancer Res. 2016 Apr 15;76(8):2376-83. | ||||
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