Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T17852 | Target Info | |||
| Target Name | Phosphodiesterase 9 (PDE9) | ||||
| Synonyms | High affinity cGMPspecific 3',5'cyclic phosphodiesterase 9A; High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | PDE9A | ||||
| Biochemical Class | Phosphoric diester hydrolase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Isobutylmethylxanthine | Ligand Info | |||
| Canonical SMILES | CC(C)CN1C2=C(C(=O)N(C1=O)C)NC=N2 | ||||
| InChI | 1S/C10H14N4O2/c1-6(2)4-14-8-7(11-5-12-8)9(15)13(3)10(14)16/h5-6H,4H2,1-3H3,(H,11,12) | ||||
| InChIKey | APIXJSLKIYYUKG-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 3758 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 3QI4 Crystal structure of PDE9A(Q453E) in complex with IBMX | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | Yes | [1] |
| PDB Sequence |
PTYPKYLLSP
190 ETIEALRKPT200 FDVWLWEPNE210 MLSCLEHMYH220 DLGLVRDFSI230 NPVTLRRWLF 240 CVHDNYRNNP250 FHNFRHCFCV260 AQMMYSMVWL270 CSLQEKFSQT280 DILILMTAAI 290 CHDLDHPGYN300 NTYQINARTE310 LAVRYNDISP320 LENHHCAVAF330 QILAEPECNI 340 FSNIPPDGFK350 QIRQGMITLI360 LATDMARHAE370 IMDSFKEKME380 NFDYSNEEHM 390 TLLKMILIKC400 CDISNEVRPM410 EVAEPWVDCL420 LEEYFMQSDR430 EKSEGLPVAP 440 FMDRDKVTKA450 TAEIGFIKFV460 LIPMFETVTK470 LFPMVEEIML480 QPLWESRDRY 490 EELKRIDDAM500 KELQK
|
|||||
|
|
||||||
| PDB ID: 2YY2 Crystal structure of the human Phosphodiesterase 9A catalytic domain complexed with IBMX | ||||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [2] |
| PDB Sequence |
PTYPKYLLSP
190 ETIEALRKPT200 FDVWLWEPNE210 MLSCLEHMYH220 DLGLVRDFSI230 NPVTLRRWLF 240 CVHDNYRNNP250 FHNFRHCFCV260 AQMMYSMVWL270 CSLQEKFSQT280 DILILMTAAI 290 CHDLDHPGYN300 NTYQINARTE310 LAVRYNDISP320 LENHHCAVAF330 QILAEPECNI 340 FSNIPPDGFK350 QIRQGMITLI360 LATDMARHAE370 IMDSFKEKME380 NFDYSNEEHM 390 TLLKMILIKC400 CDISNEVRPM410 EVAEPWVDCL420 LEEYFMQSDR430 EKSEGLPVAP 440 FMDRDKVTKA450 TAQIGFIKFV460 LIPMFETVTK470 LFPMVEEIML480 QPLWESRDRY 490 EELKRIDDAM500 KELQKK
|
|||||
|
|
||||||
| PDB ID: 2HD1 Crystal structure of PDE9 in complex with IBMX | ||||||
| Method | X-ray diffraction | Resolution | 2.23 Å | Mutation | No | [3] |
| PDB Sequence |
PTYPKYLLSP
190 ETIEALRKPT200 FDVWLWEPNE210 MLSCLEHMYH220 DLGLVRDFSI230 NPVTLRRWLF 240 CVHDNYRNNP250 FHNFRHCFCV260 AQMMYSMVWL270 CSLQEKFSQT280 DILILMTAAI 290 CHDLDHPGYN300 NTYQINARTE310 LAVRYNDISP320 LENHHCAVAF330 QILAEPECNI 340 FSNIPPDGFK350 QIRQGMITLI360 LATDMARHAE370 IMDSFKEKME380 NFDYSNEEHM 390 TLLKMILIKC400 CDISNEVRPM410 EVAEPWVDCL420 LEEYFMQSDR430 EKSEGLPVAP 440 FMDRDKVTKA450 TAQIGFIKFV460 LIPMFETVTK470 LFPMVEEIML480 QPLWESRDRY 490 EELKRIDDAM500 KELQKK
|
|||||
|
|
||||||
| PDB ID: 3N3Z Crystal structure of PDE9A (E406A) mutant in complex with IBMX | ||||||
| Method | X-ray diffraction | Resolution | 2.75 Å | Mutation | Yes | [4] |
| PDB Sequence |
PTYPKYLLSP
190 ETIEALRKPT200 FDVWLWEPNE210 MLSCLEHMYH220 DLGLVRDFSI230 NPVTLRRWLF 240 CVHDNYRNNP250 FHNFRHCFCV260 AQMMYSMVWL270 CSLQEKFSQT280 DILILMTAAI 290 CHDLDHPGYN300 NTYQINARTE310 LAVRYNDISP320 LENHHCAVAF330 QILAEPECNI 340 FSNIPPDGFK350 QIRQGMITLI360 LATDMARHAE370 IMDSFKEKME380 NFDYSNEEHM 390 TLLKMILIKC400 CDISNAVRPM410 EVAEPWVDCL420 LEEYFMQSDR430 EKSEGLPVAP 440 FMDRDKVTKA450 TAQIGFIKFV460 LIPMFETVTK470 LFPMVEEIML480 QPLWESRDRY 490 EELKRIDDAM500 KELQKK
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .IBM or .IBM2 or .IBM3 or :3IBM;style chemicals stick;color identity;select .A:251 or .A:365 or .A:402 or .A:403 or .A:405 or .A:406 or .A:417 or .A:420 or .A:421 or .A:424 or .A:441 or .A:452 or .A:453 or .A:456; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural asymmetry of phosphodiesterase-9, potential protonation of a glutamic acid, and role of the invariant glutamine. PLoS One. 2011 Mar 31;6(3):e18092. | ||||
| REF 2 | Crystal structure of the human Phosphodiesterase 9A catalytic domain | ||||
| REF 3 | Crystal structure of phosphodiesterase 9 shows orientation variation of inhibitor 3-isobutyl-1-methylxanthine binding. Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9624-9. | ||||
| REF 4 | Crystal structure of PDE9A (E406A) mutation in complex with IBMX | ||||
If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.