Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T61657 | Target Info | |||
| Target Name | Retinoic acid receptor beta (RARB) | ||||
| Synonyms | RAR-epsilon; RAR-beta; Nuclear receptor subfamily 1 group B member 2; NR1B2; HBV-activated protein; HAP | ||||
| Target Type | Successful Target | ||||
| Gene Name | RARB | ||||
| Biochemical Class | Nuclear hormone receptor | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Tretinoin | Ligand Info | |||||
| Structure Description | Crystal structure of RARb LBD in complex with 9cis retinoic acid | PDB:4DM8 | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
ESYEMTAELD
187 DLTEKIRKAH197 QETFPSLCQL207 GKYTTNSSAD217 HRVRLDLGLW227 DKFSELATKC 237 IIKIVEFAKR247 LPGFTGLTIA257 DQITLLKAAC267 LDILILRICT277 RYTPEQDTMT 287 FSDGLTLNRT297 QMHNAGFGPL307 TDLVFTFANQ317 LLPLEMDDTE327 TGLLSAICLI 337 CGDRQDLEEP347 TKVDKLQEPL357 LEALKIYIRK367 RRPPHMFPKI379 LMKITDLRSI 389 SAKGAERVIT399 LKMEIPGSMP409 PLIQEMLE
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PHE201
3.435
TRP227
4.222
PHE230
3.693
LEU233
3.327
ALA234
3.546
CYS237
3.927
LYS240
4.954
LEU268
3.826
LEU271
3.529
ILE272
3.612
ILE275
4.059
ARG278
2.823
THR287
4.356
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: BMS641 | Ligand Info | |||||
| Structure Description | Crystal structure of RARbeta LBD in complex with selective partial agonist BMS641 [3-chloro-4-[(E)-2-(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)ethenyl]benzoic acid] | PDB:4JYI | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [2] |
| PDB Sequence |
SYEMTAELDD
179 LTEKIRKAHQ189 ETFPSLCQLG199 KYTTNSSADH209 RVRLDLGLWD219 KFSELATKCI 229 IKIVEFAKRL239 PGFTGLTIAD249 QITLLKAACL259 DILILRICTR269 YTPEQDTMTF 279 SDGLTLNRTQ289 MHNAGFGPLT299 DLVFTFANQL309 LPLEMDDTET319 GLLSAICLIC 329 GDRQDLEEPT339 KVDKLQEPLL349 EALKIYIRKR359 RPSKPHMFPK369 ILMKITDLRS 379 ISAKGAERVI389 TLKMEIPGSM399 PPLIQEMME
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PHE192
3.107
TRP218
3.932
PHE221
3.262
LEU224
3.789
ALA225
3.338
CYS228
3.656
LEU259
3.745
LEU262
3.498
ILE263
3.749
ARG265
4.479
ILE266
3.736
ARG269
3.395
PHE279
3.300
|
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| Ligand Name: TTNPB | Ligand Info | |||||
| Structure Description | Crystal structure of RARb LBD homodimer in complex with TTNPB | PDB:4DM6 | ||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [1] |
| PDB Sequence |
ESYEMTAELD
187 DLTEKIRKAH197 QETFPSLCQL207 GKYTTNSSAD217 HRVRLDLGLW227 DKFSELATKC 237 IIKIVEFAKR247 LPGFTGLTIA257 DQITLLKAAC267 LDILILRICT277 RYTPEQDTMT 287 FSDGLTLNRT297 QMHNAGFGPL307 TDLVFTFANQ317 LLPLEMDDTE327 TGLLSAICLI 337 CGDRQDLEEP347 TKVDKLQEPL357 LEALKIYIRK367 RRPSKPHMFP377 KILMKITDLR 387 SISAKGAERV397 ITLKMEIPGS407 MPPLIQEMLE417
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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 .TTB or .TTB2 or .TTB3 or :3TTB;style chemicals stick;color identity;select .A:201 or .A:227 or .A:230 or .A:233 or .A:234 or .A:237 or .A:268 or .A:271 or .A:272 or .A:274 or .A:275 or .A:278 or .A:287 or .A:288 or .A:289 or .A:290 or .A:303 or .A:304 or .A:307 or .A:393 or .A:396 or .A:397 or .A:400 or .A:408 or .A:412 or .A:416; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PHE201
3.008
TRP227
4.231
PHE230
3.530
LEU233
3.568
ALA234
3.541
CYS237
3.949
LEU268
3.867
LEU271
3.217
ILE272
3.576
ARG274
4.464
ILE275
3.546
ARG278
3.113
THR287
4.985
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: LG100754 | Ligand Info | |||||
| Structure Description | Crystal structure of RARbeta LBD in complex with LG 100754 | PDB:6SSQ | ||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [3] |
| PDB Sequence |
SYEMTAELDD
179 LTEKIRKAHQ189 ETFPSLCQLG199 KYTTNSSADH209 RVRLDLGLWD219 KFSELATKCI 229 IKIVEFAKRL239 PGFTGLTIAD249 QITLLKAACL259 DILILRICTR269 YTPEQDTMTF 279 SDGLTLNRTQ289 MHNAGFGPLT299 DLVFTFANQL309 LPLEMDDTET319 GLLSAICLIC 329 GDRQDLEEPT339 KVDKLQEPLL349 EALKIYIRKR359 RPSKPHMFPK369 ILMKITDLRS 379 ISAKGAERVI389 TLKMEIPGSM399 PPLIQEMME
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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 .754 or .7542 or .7543 or :3754;style chemicals stick;color identity;select .A:192 or .A:218 or .A:221 or .A:222 or .A:224 or .A:225 or .A:228 or .A:259 or .A:262 or .A:263 or .A:265 or .A:266 or .A:269 or .A:279 or .A:280 or .A:294 or .A:295 or .A:298 or .A:302 or .A:380 or .A:384 or .A:387 or .A:388 or .A:391 or .A:399 or .A:403 or .A:407; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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PHE192
3.351
TRP218
4.315
PHE221
3.843
SER222
4.729
LEU224
3.740
ALA225
3.426
CYS228
3.786
LEU259
3.738
LEU262
3.369
ILE263
3.438
ARG265
4.037
ILE266
3.948
ARG269
3.564
PHE279
3.490
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| Ligand Name: Benzoic acid, 4-(((5,6-dihydro-5,5-dimethyl-8-phenyl-2-naphthalenyl)carbonyl)amino)- | Ligand Info | |||||
| Structure Description | Crystal structure of RARbeta LBD in complex with agonist BMS411 [4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid] | PDB:4JYG | ||||
| Method | X-ray diffraction | Resolution | 2.35 Å | Mutation | No | [2] |
| PDB Sequence |
SYEMTAELDD
179 LTEKIRKAHQ189 ETFPSLCQLG199 KYTTNSSADH209 RVRLDLGLWD219 KFSELATKCI 229 IKIVEFAKRL239 PGFTGLTIAD249 QITLLKAACL259 DILILRICTR269 YTPEQDTMTF 279 SDGLTLNRTQ289 MHNAGFGPLT299 DLVFTFANQL309 LPLEMDDTET319 GLLSAICLIC 329 GDRQDLEEPT339 KVDKLQEPLL349 EALKIYIRKR359 RPSKPHMFPK369 ILMKITDLRS 379 ISAKGAERVI389 TLKMEIPGSM399 PPLIQEMME
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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 .1NY or .1NY2 or .1NY3 or :31NY;style chemicals stick;color identity;select .A:192 or .A:218 or .A:221 or .A:224 or .A:225 or .A:228 or .A:259 or .A:262 or .A:263 or .A:265 or .A:266 or .A:269 or .A:278 or .A:279 or .A:280 or .A:295 or .A:298 or .A:302 or .A:380 or .A:384 or .A:387 or .A:388 or .A:391 or .A:399 or .A:403 or .A:407; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
PHE192
3.741
TRP218
3.826
PHE221
3.511
LEU224
3.742
ALA225
3.119
CYS228
3.725
LEU259
3.850
LEU262
3.225
ILE263
3.915
ARG265
4.292
ILE266
3.460
ARG269
3.028
THR278
4.854
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| Ligand Name: 4-{[(8-Phenylnaphthalen-2-Yl)carbonyl]amino}benzoic Acid | Ligand Info | |||||
| Structure Description | Crystal structure of RARbeta LBD in complex with selective agonist BMS948 [4-{[(8-phenylnaphthalen-2-yl)carbonyl]amino}benzoic acid] | PDB:4JYH | ||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [2] |
| PDB Sequence |
SYEMTAELDD
179 LTEKIRKAHQ189 ETFPSLCQLG199 KYTTNSSADH209 RVRLDLGLWD219 KFSELATKCI 229 IKIVEFAKRL239 PGFTGLTIAD249 QITLLKAACL259 DILILRICTR269 YTPEQDTMTF 279 SDGLTLNRTQ289 MHNAGFGPLT299 DLVFTFANQL309 LPLEMDDTET319 GLLSAICLIC 329 GDRQDLEEPT339 KVDKLQEPLL349 EALKIYIRKR359 RPSKPHMFPK369 ILMKITDLRS 379 ISAKGAERVI389 TLKMEIPGSM399 PPLIQEMME
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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 .JYH or .JYH2 or .JYH3 or :3JYH;style chemicals stick;color identity;select .A:192 or .A:218 or .A:221 or .A:224 or .A:225 or .A:228 or .A:259 or .A:262 or .A:263 or .A:265 or .A:266 or .A:269 or .A:278 or .A:279 or .A:280 or .A:295 or .A:298 or .A:302 or .A:384 or .A:388 or .A:391 or .A:399 or .A:403 or .A:407; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
PHE192
4.036
TRP218
4.113
PHE221
3.531
LEU224
3.385
ALA225
3.119
CYS228
3.638
LEU259
3.796
LEU262
3.276
ILE263
3.726
ARG265
4.336
ILE266
3.470
ARG269
2.800
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis for a molecular allosteric control mechanism of cofactor binding to nuclear receptors. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):E588-94. | ||||
| REF 2 | An Unexpected Mode Of Binding Defines BMS948 as A Full Retinoic Acid Receptor beta (RARbeta, NR1B2) Selective Agonist. PLoS One. 2015 May 1;10(5):e0123195. | ||||
| REF 3 | Regulation of RXR-RAR Heterodimers by RXR- and RAR-Specific Ligands and Their Combinations. Cells. 2019 Nov 5;8(11):1392. | ||||
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