Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T26748 | Target Info | |||
| Target Name | Diphosphoinositol polyphosphate phosphohydrolase 2 (NUDT3) | ||||
| Synonyms | NUDT3; Diphosphoinositol polyphosphate phosphohydrolase; DIPP2 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | NUDT3 | ||||
| Biochemical Class | Acid anhydrides hydrolase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Myo-inositol hexaphosphate | Ligand Info | |||
| Canonical SMILES | C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O | ||||
| InChI | 1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24) | ||||
| InChIKey | IMQLKJBTEOYOSI-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 890 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6WOD Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 2min in the absence of Fluoride. | ||||||
| Method | X-ray diffraction | Resolution | 1.35 Å | Mutation | No | [1] |
| PDB Sequence |
TRTYDGDGYK
18 KRAACLCFRS28 ESEEEVLLVS38 SSRHPDRWIV48 PGGGMEPEEE58 PSVAAVREVC 68 EEAGVKGTLG78 RLVGIFENQE88 RKHRTYVYVL98 IVTEVLEDWE108 DSVNIGRKRE 118 WFKIEDAIKV128 LQYHKPVQAS138 YFET
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| PDB ID: 6WOE Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 10min in the absence of Fluoride. | ||||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | No | [1] |
| PDB Sequence |
TRTYDGDGYK
18 KRAACLCFRS28 ESEEEVLLVS38 SSRHPDRWIV48 PGGGMEPEEE58 PSVAAVREVC 68 EEAGVKGTLG78 RLVGIFENQE88 RKHRTYVYVL98 IVTEVLEDWE108 DSVNIGRKRE 118 WFKIEDAIKV128 LQYHKPVQAS138 YFET
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| PDB ID: 6WOF Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 20min in the absence of Fluoride. | ||||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [1] |
| PDB Sequence |
RTYDGDGYKK
19 RAACLCFRSE29 SEEEVLLVSS39 SRHPDRWIVP49 GGGMEPEEEP59 SVAAVREVCE 69 EAGVKGTLGR79 LVGIFENQER89 KHRTYVYVLI99 VTEVLEDWED109 SVNIGRKREW 119 FKIEDAIKVL129 QYHKPVQASY139 FET
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| PDB ID: 2FVV Human Diphosphoinositol polyphosphate phosphohydrolase 1 | ||||||
| Method | X-ray diffraction | Resolution | 1.25 Å | Mutation | No | [2] |
| PDB Sequence |
QTRTYDGDGY
17 KKRAACLCFR27 SESEEEVLLV37 SSSRHPDRWI47 VPGGGMEPEE57 EPSVAAVREV 67 CEEAGVKGTL77 GRLVGIFENQ87 ERKHRTYVYV97 LIVTEVLEDW107 EDSVNIGRKR 117 EWFKIEDAIK127 VLQYHKPVQA137 SYFET
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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 .IHP or .IHP2 or .IHP3 or :3IHP;style chemicals stick;color identity;select .A:10 or .A:18 or .A:20 or .A:39 or .A:40 or .A:41 or .A:47 or .A:51 or .A:52 or .A:86 or .A:89 or .A:91 or .A:115 or .A:133; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 2Q9P Human diphosphoinositol polyphosphate phosphohydrolase 1, Mg-F complex | ||||||
| Method | X-ray diffraction | Resolution | 1.65 Å | Mutation | No | [2] |
| PDB Sequence |
RTYDGDGYKK
19 RAACLCFRSE29 SEEEVLLVSS39 SRHPDRWIVP49 GGGMEPEEEP59 SVAAVREVCE 69 EAGVKGTLGR79 LVGIFENQER89 KHRTYVYVLI99 VTEVLEDWED109 SVNIGRKREW 119 FKIEDAIKVL129 QYHKPVQASY139 FE
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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 .IHP or .IHP2 or .IHP3 or :3IHP;style chemicals stick;color identity;select .A:10 or .A:18 or .A:20 or .A:38 or .A:39 or .A:40 or .A:41 or .A:42 or .A:47 or .A:50 or .A:51 or .A:52 or .A:70 or .A:89 or .A:91 or .A:115 or .A:133; 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 | New structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1. FASEB J. 2021 Feb;35(2):e21275. | ||||
| REF 2 | Crystal structure of human diphosphoinositol phosphatase 1. Proteins. 2009 Oct;77(1):242-6. | ||||
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