Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T10265 | Target Info | |||
| Target Name | Phosphodiesterase 4B (PDE4B) | ||||
| Synonyms | cAMP-specific 3',5'-cyclic phosphodiesterase 4B; Type 4B cAMP phosphodiesterase; Type 4 cyclic adenosine monophosphate phosphodiesterase (type 4 PDE); PDE32; DPDE4 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | PDE4B | ||||
| Biochemical Class | Phosphoric diester hydrolase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Arsenic | Ligand Info | |||
| Canonical SMILES | [As] | ||||
| InChI | 1S/As | ||||
| InChIKey | RQNWIZPPADIBDY-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 5359596 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1RO6 Crystal structure of PDE4B2B complexed with Rolipram (R & S) | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [1] |
| PDB Sequence |
SISRFGVNTE
161 NEDHLAKELE171 DLNKWGLNIF181 NVAGYSHNRP191 LTCIMYAIFQ201 ERDLLKTFRI 211 SSDTFITYMM221 TLEDHYHSDV231 AYHNSLHAAD241 VAQSTHVLLS251 TPALDAVFTD 261 LEILAAIFAA271 AIHDVDHPGV281 SNQFLINTNS291 ELALMYNDES301 VLENHHLAVG 311 FKLLQEEHCD321 IFMNLTKKQR331 QTLRKMVIDM341 VLATDMSKHM351 SLLADLKTMV 361 ETKKVTSSGV371 LLLDNYTDRI381 QVLRNMVHCA391 DLSNPTKSLE401 LYRQWTDRIM 411 EEFFQQGDKE421 RERGMEISPM431 CDKHTASVEK441 SQVGFIDYIV451 HPLWETWADL 461 VQPDAQDILD471 TLEDNRNWYQ481 SMIPQAPAPP491 LDEQ
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| PDB ID: 1F0J CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B2B | ||||||
| Method | X-ray diffraction | Resolution | 1.77 Å | Mutation | Yes | [2] |
| PDB Sequence |
SISRFGVNTE
161 NEDHLAKELE171 DLNKWGLNIF181 NVAGYSHNRP191 LTCIMYAIFQ201 ERDLLKTFRI 211 SSDTFITYMM221 TLEDHYHSDV231 AYHNSLHAAD241 VAQSTHVLLS251 TPALDAVFTD 261 LEILAAIFAA271 AIHDVDHPGV281 SNQFLINTNS291 ELALMYNDES301 VLENHHLAVG 311 FKLLQEEHCD321 IFMNLTKKQR331 QTLRKMVIDM341 VLATDMSKHM351 SLLADLKTMV 361 ETKKVTSSGV371 LLLDNYTDRI381 QVLRNMVHCA391 DLSNPTKSLE401 LYRQWTDRIM 411 EEFFQQGDKE421 RERGMEISPM431 CDKHTASVEK441 SQVGFIDYIV451 HPLWETWADL 461 VQPDAQDILD471 TLEDNRNWYQ481 SMIPQAPANR497 DCQGLMEKFQ507 F |
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| PDB ID: 3FRG Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with a Quinoline Inhibitor | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [3] |
| PDB Sequence |
ISRFGVNTEN
162 EDHLAKELED172 LNKWGLNIFN182 VAGYSHNRPL192 TCIMYAIFQE202 RDLLKTFRIS 212 SDTFITYMMT222 LEDHYHSDVA232 YHNSLHAADV242 AQSTHVLLST252 PALDAVFTDL 262 EILAAIFAAA272 IHDVDHPGVS282 NQFLINTNSE292 LALMYNDESV302 LENHHLAVGF 312 KLLQEEHCDI322 FMNLTKKQRQ332 TLRKMVIDMV342 LATDMSKHMS352 LLADLKTMVE 362 TKKVTSSGVL372 LLDNYTDRIQ382 VLRNMVHCAD392 LSNPTKSLEL402 YRQWTDRIME 412 EFFQQGDKER422 ERGMEISPMC432 DKHTASVEKS442 QVGFIDYIVH452 PLWETWADLV 462 QPDAQDILDT472 LEDNRNWYQA482 MIPQA
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| PDB ID: 3D3P Crystal structure of PDE4B catalytic domain in complex with a pyrazolopyridine inhibitor | ||||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | Yes | [4] |
| PDB Sequence |
SISRFGVNTE
161 NEDHLAKELE171 DLNKWGLNIF181 NVAGYSHNRP191 LTCIMYAIFQ201 ERDLLKTFRI 211 SSDTFITYMM221 TLEDHYHSDV231 AYHNSLHAAD241 VAQSTHVLLS251 TPALDAVFTD 261 LEILAAIFAA271 AIHDVDHPGV281 SNQFLINTNS291 ELALMYNDES301 VLENHHLAVG 311 FKLLQEEHCD321 IFMNLTKKQR331 QTLRKMVIDM341 VLATDMSKHM351 SLLADLKTMV 361 ETKKVTSSGV371 LLLDNYTDRI381 QVLRNMVHCA391 DLSNPTKSLE401 LYRQWTDRIM 411 EEFFQQGDKE421 RERGMEISPM431 CDKHTASVEK441 SQVGFIDYIV451 HPLWETWADL 461 VQPDAQDILD471 TLEDNRNWYQ481 AMIPQA
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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 .ARS or .ARS2 or .ARS3 or :3ARS;style chemicals stick;color identity;select .A:153 or .A:166 or .A:170 or .A:194 or .A:197 or .A:218 or .A:222 or .A:314 or .A:317 or .A:319 or .A:320 or .A:414 or .A:417 or .A:429 or .A:431 or .A:432; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 3GWT Catalytic domain of human phosphodiesterase 4B2B in complex with a quinoline inhibitor | ||||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | Yes | [5] |
| PDB Sequence |
SISRFGVNTE
161 NEDHLAKELE171 DLNKWGLNIF181 NVAGYSHNRP191 LTCIMYAIFQ201 ERDLLKTFRI 211 SSDTFITYMM221 TLEDHYHSDV231 AYHNSLHAAD241 VAQSTHVLLS251 TPALDAVFTD 261 LEILAAIFAA271 AIHDVDHPGV281 SNQFLINTNS291 ELALMYNDES301 VLENHHLAVG 311 FKLLQEEHCD321 IFMNLTKKQR331 QTLRKMVIDM341 VLATDMSKHM351 SLLADLKTMV 361 ETKKVTSSGV371 LLLDNYTDRI381 QVLRNMVHCA391 DLSNPTKSLE401 LYRQWTDRIM 411 EEFFQQGDKE421 RERGMEISPM431 CDKHTASVEK441 SQVGFIDYIV451 HPLWETWADL 461 VQPDAQDILD471 TLEDNRNWYQ481 AMIPQA
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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 .ARS or .ARS2 or .ARS3 or :3ARS;style chemicals stick;color identity;select .A:153 or .A:166 or .A:170 or .A:194 or .A:197 or .A:218 or .A:222 or .A:233 or .A:234 or .A:238 or .A:275 or .A:314 or .A:317 or .A:319 or .A:320 or .A:392 or .A:414 or .A:417 or .A:429 or .A:431 or .A:432; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ILE153
4.491
LEU166
4.535
LEU170
4.490
CYS194
2.271
TYR197
4.313
THR218
4.974
THR222
4.959
TYR233
4.236
HIS234
3.282
HIS238
4.461
ASP275
4.828
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| PDB ID: 3O57 Catalytic domain of human phosphodiesterase 4b2b in complex with a 5-heterocycle pyrazolopyridine inhibitor | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [6] |
| PDB Sequence |
SISRFGVNTE
161 NEDHLAKELE171 DLNKWGLNIF181 NVAGYSHNRP191 LTCIMYAIFQ201 ERDLLKTFRI 211 SSDTFITYMM221 TLEDHYHSDV231 AYHNSLHAAD241 VAQSTHVLLS251 TPALDAVFTD 261 LEILAAIFAA271 AIHDVDHPGV281 SNQFLINTNS291 ELALMYNDES301 VLENHHLAVG 311 FKLLQEEHCD321 IFMNLTKKQR331 QTLRKMVIDM341 VLATDMSKHM351 SLLADLKTMV 361 ETKKVTSSGV371 LLLDNYTDRI381 QVLRNMVHCA391 DLSNPTKSLE401 LYRQWTDRIM 411 EEFFQQGDKE421 RERGMEISPM431 CDKHTASVEK441 SQVGFIDYIV451 HPLWETWADL 461 VQPDAQDILD471 TLEDNRNWYQ481 AMIPQA
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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 .ARS or .ARS2 or .ARS3 or :3ARS;style chemicals stick;color identity;select .A:153 or .A:156 or .A:166 or .A:170 or .A:194 or .A:197 or .A:218 or .A:222 or .A:314 or .A:317 or .A:319 or .A:320 or .A:414 or .A:417 or .A:429 or .A:431 or .A:432; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 3O56 Catalytic domain of human phosphodiesterase 4b2b in complex with a 5-heterocycle pyrazolopyridine inhibitor | ||||||
| Method | X-ray diffraction | Resolution | 2.42 Å | Mutation | Yes | [6] |
| PDB Sequence |
ISRFGVNTEN
162 EDHLAKELED172 LNKWGLNIFN182 VAGYSHNRPL192 TCIMYAIFQE202 RDLLKTFRIS 212 SDTFITYMMT222 LEDHYHSDVA232 YHNSLHAADV242 AQSTHVLLST252 PALDAVFTDL 262 EILAAIFAAA272 IHDVDHPGVS282 NQFLINTNSE292 LALMYNDESV302 LENHHLAVGF 312 KLLQEEHCDI322 FMNLTKKQRQ332 TLRKMVIDMV342 LATDMSKHMS352 LLADLKTMVE 362 TKKVTSSGVL372 LLDNYTDRIQ382 VLRNMVHCAD392 LSNPTKSLEL402 YRQWTDRIME 412 EFFQQGDKER422 ERGMEISPMC432 DKHTASVEKS442 QVGFIDYIVH452 PLWETWADLV 462 QPDAQDILDT472 LEDNRNWYQA482 MIPQA
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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 .ARS or .ARS2 or .ARS3 or :3ARS;style chemicals stick;color identity;select .A:153 or .A:156 or .A:170 or .A:194 or .A:197 or .A:198 or .A:314 or .A:317 or .A:319 or .A:320 or .A:414 or .A:417 or .A:429 or .A:431 or .A:432; 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 | Crystal structures of the catalytic domain of phosphodiesterase 4B complexed with AMP, 8-Br-AMP, and rolipram. J Mol Biol. 2004 Mar 19;337(2):355-65. | ||||
| REF 2 | Atomic structure of PDE4: insights into phosphodiesterase mechanism and specificity. Science. 2000 Jun 9;288(5472):1822-5. | ||||
| REF 3 | Quinolines as a novel structural class of potent and selective PDE4 inhibitors: optimisation for oral administration. Bioorg Med Chem Lett. 2009 Mar 1;19(5):1380-5. | ||||
| REF 4 | Pyrazolopyridines as a novel structural class of potent and selective PDE4 inhibitors. Bioorg Med Chem Lett. 2008 Jul 15;18(14):4237-41. | ||||
| REF 5 | Quinolines as a novel structural class of potent and selective PDE4 inhibitors. Optimisation for inhaled administration. Bioorg Med Chem Lett. 2009 Sep 1;19(17):5261-5. | ||||
| REF 6 | Pyrazolopyridines as potent PDE4B inhibitors: 5-heterocycle SAR. Bioorg Med Chem Lett. 2010 Oct 1;20(19):5803-6. | ||||
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