Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T88975 | Target Info | |||
| Target Name | Phosphodiesterase 3A (PDE3A) | ||||
| Synonyms | cGMP-inhibited 3',5'-cyclic phosphodiesterase A; Phosphodiesterase 3A; Cyclic GMP-inhibited phosphodiesterase A; Cyclic GMP inhibited phosphodiesterase A; CGI-PDE A | ||||
| Target Type | Successful Target | ||||
| Gene Name | PDE3A | ||||
| Biochemical Class | Phosphoric diester hydrolase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Anagrelide | Ligand Info | |||||
| Structure Description | Cryo-EM structure of anagrelide-induced PDE3A-SLFN12 complex | PDB:7EG0 | ||||
| Method | Electron microscopy | Resolution | 3.40 Å | Mutation | Yes | [1] |
| PDB Sequence |
KPILAPEPLV
678 MDNLDSIMEQ688 LNTWNFPIFD698 LVENIGRKCG708 RILSQVSYRL718 FEDMGLFEAF 728 KIPIREFMNY738 FHALEIGYRD748 IPYHNRIHAT758 DVLHAVWYLT768 TQPIPGLSTV 778 GYVFSKTYNV809 TDDKYGCLSG819 NIPALELMAL829 YVAAAMHDYD839 HPGRTNAFLV 849 ATSAPQAVLY859 NDRSVLENHH869 AAAAWNLFMS879 RPEYNFLINL889 DHVEFKHFRF 899 LVIEAILATD909 LKKHFDFVAK919 FNGKVNDDVG929 IDWTNENDRL939 LVCQMCIKLA 949 DINGPAKCKE959 LHLQWTDGIV969 NEFYEQGDEE979 ASLGLPISPF989 MDRSAPQLAN 999 LQESFISHIV1009 GPLCNSYDSA1019 GLMPGKWVEK1070 IYCQITQHLL1080 QNHKMWKKVI 1090 EEEQRLAGIE1100 NQ
|
|||||
|
|
||||||
| Ligand Name: Adenosine monophosphate | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human PDE3A bound to AMP | PDB:7L29 | ||||
| Method | X-ray diffraction | Resolution | 2.08 Å | Mutation | No | [2] |
| PDB Sequence |
KPILAPEPLV
678 MDNLDSIMEQ688 LNTWNFPIFD698 LVENIGRKCG708 RILSQVSYRL718 FEDMGLFEAF 728 KIPIREFMNY738 FHALEIGYRD748 IPYHNRIHAT758 DVLHAVWYLT768 TQPIPGLSTV 778 IGGSYVFSKT806 YNVTDDKYGC816 LSGNIPALEL826 MALYVAAAMH836 DYDHPGRTNA 846 FLVATSAPQA856 VLYNDRSVLE866 NHHAAAAWNL876 FMSRPEYNFL886 INLDHVEFKH 896 FRFLVIEAIL906 ATDLKKHFDF916 VAKFNGKVND926 DVGIDWTNEN936 DRLLVCQMCI 946 KLADINGPAK956 CKELHLQWTD966 GIVNEFYEQG976 DEEASLGLPI986 SPFMDRSAPQ 996 LANLQESFIS1006 HIVGPLCNSY1016 DSAGLMPGKW1026 VRKIYCQITQ1077 HLLQNHKMWK 1087 KVIEEE
|
|||||
|
|
||||||
| Ligand Name: Parvine | Ligand Info | |||||
| Structure Description | Cryo-EM structure of nauclefine-induced PDE3A-SLFN12 complex | PDB:7EG4 | ||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | Yes | [1] |
| PDB Sequence |
KPILAPEPLV
678 MDNLDSIMEQ688 LNTWNFPIFD698 LVENIGRKCG708 RILSQVSYRL718 FEDMGLFEAF 728 KIPIREFMNY738 FHALEIGYRD748 IPYHNRIHAT758 DVLHAVWYLT768 TQPIPGLSTV 778 GYVFSKTYNV809 TDDKYGCLSG819 NIPALELMAL829 YVAAAMHDYD839 HPGRTNAFLV 849 ATSAPQAVLY859 NDRSVLENHH869 AAAAWNLFMS879 RPEYNFLINL889 DHVEFKHFRF 899 LVIEAILATD909 LKKHFDFVAK919 FNGKVNDDVG929 IDWTNENDRL939 LVCQMCIKLA 949 DINGPAKCKE959 LHLQWTDGIV969 NEFYEQGDEE979 ASLGLPISPF989 MDRSAPQLAN 999 LQESFISHIV1009 GPLCNSYDSA1019 GLMPGKWVEK1070 IYCQITQHLL1080 QNHKMWKKVI 1090 EEEQRLAGIE1100 NQ
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .J36 or .J362 or .J363 or :3J36;style chemicals stick;color identity;select .C:751 or .C:752 or .C:844 or .C:910 or .C:950 or .C:951 or .C:952 or .C:953 or .C:954 or .C:961 or .C:964 or .C:965 or .C:968 or .C:972 or .C:1000 or .C:1001 or .C:1004; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: (R)-Dnmdp | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human PDE3A bound to DNMDP | PDB:7KWE | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [2] |
| PDB Sequence |
KPILAPEPLV
678 MDNLDSIMEQ688 LNTWNFPIFD698 LVENIGRKCG708 RILSQVSYRL718 FEDMGLFEAF 728 KIPIREFMNY738 FHALEIGYRD748 IPYHNRIHAT758 DVLHAVWYLT768 TQPIPGLSTV 778 SYVFSKTYNV809 TDDKYGCLSG819 NIPALELMAL829 YVAAAMHDYD839 HPGRTNAFLV 849 ATSAPQAVLY859 NDRSVLENHH869 AAAAWNLFMS879 RPEYNFLINL889 DHVEFKHFRF 899 LVIEAILATD909 LKKHFDFVAK919 FNGKVNDDVG929 IDWTNENDRL939 LVCQMCIKLA 949 DINGPAKCKE959 LHLQWTDGIV969 NEFYEQGDEE979 ASLGLPISPF989 MDRSAPQLAN 999 LQESFISHIV1009 GPLCNSYDSA1019 GLMPGKWVRK1070 IYCQITQHLL1080 QNHKMWKKVI 1090 EEE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .X5M or .X5M2 or .X5M3 or :3X5M;style chemicals stick;color identity;select .A:751 or .A:752 or .A:844 or .A:910 or .A:950 or .A:951 or .A:953 or .A:954 or .A:961 or .A:964 or .A:965 or .A:968 or .A:972 or .A:1000 or .A:1001 or .A:1004; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (2E)-9,10-dimethoxy-3-methyl-2-[(2,4,6-trimethylphenyl)imino]-2,3,6,7-tetrahydro-4H-pyrimido[6,1-a]isoquinolin-4-one | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of human PDE3A bound to Trequinsin | PDB:7L28 | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [2] |
| PDB Sequence |
KPILAPEPLV
678 MDNLDSIMEQ688 LNTWNFPIFD698 LVENIGRKCG708 RILSQVSYRL718 FEDMGLFEAF 728 KIPIREFMNY738 FHALEIGYRD748 IPYHNRIHAT758 DVLHAVWYLT768 TQPIPGLSTV 778 SYVFSKTYNV809 TDDKYGCLSG819 NIPALELMAL829 YVAAAMHDYD839 HPGRTNAFLV 849 ATSAPQAVLY859 NDRSVLENHH869 AAAAWNLFMS879 RPEYNFLINL889 DHVEFKHFRF 899 LVIEAILATD909 LKKHFDFVAK919 FNGKVNDDVG929 IDWTNENDRL939 LVCQMCIKLA 949 DINGPAKCKE959 LHLQWTDGIV969 NEFYEQGDEE979 ASLGLPISPF989 MDRSAPQLAN 999 LQESFISHIV1009 GPLCNSYDSA1019 GLMPGKWVRK1070 IYCQITQHLL1080 QNHKMWKKVI 1090 EEE
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .XKG or .XKG2 or .XKG3 or :3XKG;style chemicals stick;color identity;select .A:751 or .A:752 or .A:844 or .A:910 or .A:951 or .A:953 or .A:954 or .A:968 or .A:972 or .A:988 or .A:989 or .A:1000 or .A:1001 or .A:1003 or .A:1004 or .A:1007 or .A:1008; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells. Nat Commun. 2021 Oct 27;12(1):6204. | ||||
| REF 2 | Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Nat Commun. 2021 Jul 16;12(1):4375. | ||||
If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.