Target Binding Site Detail
| 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 | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | (R)-Dnmdp | Ligand Info | |||
| Canonical SMILES | CCN(CC)C1=C(C=C(C=C1)C2=NNC(=O)CC2C)[N+](=O)[O-] | ||||
| InChI | 1S/C15H20N4O3/c1-4-18(5-2)12-7-6-11(9-13(12)19(21)22)15-10(3)8-14(20)16-17-15/h6-7,9-10H,4-5,8H2,1-3H3,(H,16,20)/t10-/m1/s1 | ||||
| InChIKey | YOSSKNZHADPXJX-SNVBAGLBSA-N | ||||
| PubChem Compound ID | 7122097 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 7LRC Cryo-EM of the SLFN12-PDE3A complex: PDE3A body refinement | ||||||
| Method | Electron microscopy | Resolution | 2.97 Å | Mutation | No | [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 GLMPGKWVER1069 KIYCQITQHL1079 LQNHKMWKKV 1089 IEEEQRLAGI1099 E
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| PDB ID: 7LRD Cryo-EM of the SLFN12-PDE3A complex: Consensus subset model | ||||||
| Method | Electron microscopy | Resolution | 3.22 Å | Mutation | No | [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 GLMPGKWVER1069 KIYCQITQHL1079 LQNHKMWKKV 1089 IEEEQRLAGI1099 E
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| PDB ID: 7EG1 Cryo-EM structure of DNMDP-induced PDE3A-SLFN12 complex | ||||||
| Method | Electron microscopy | Resolution | 3.20 Å | Mutation | Yes | [2] |
| 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
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| PDB ID: 7KWE Crystal structure of the catalytic domain of human PDE3A bound to DNMDP | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| 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
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Click to Show 3D Structure of This Binding Site
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Nat Commun. 2021 Jul 16;12(1):4375. | ||||
| REF 2 | 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. | ||||
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