Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T73184 | Target Info | |||
| Target Name | Histone-lysine N-methyltransferase SETD7 (SETD7) | ||||
| Synonyms | SET9; SET7/9; SET7; SET domain-containing protein 7; Lysine N-methyltransferase 7; KMT7; KIAA1717; Histone H3-K4 methyltransferase SETD7; H3-K4-HMTase SETD7 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | SETD7 | ||||
| Biochemical Class | Methyltransferase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Ademetionine | Ligand Info | |||
| Canonical SMILES | C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)N2C=NC3=C(N=CN=C32)N)O)O | ||||
| InChI | 1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27?/m0/s1 | ||||
| InChIKey | MEFKEPWMEQBLKI-AIRLBKTGSA-N | ||||
| PubChem Compound ID | 34755 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1N6C Structure of SET7/9 | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
GGVLQGTYVD
88 GELNGPAQEY98 DTDGRLIFKG108 QYKDNIRHGV118 CWIYYPDGGS128 LVGEVNEDGE 138 MTGEKIAYVY148 PDERTALYGK158 FIDGEMIEGK168 LATLMSTEEG178 RPHFELMPGN 188 SVYHFDKSTS198 SCISTNALLP208 DPYESERVYV218 AESLISSAGE228 GLFSKVAVGP 238 NTVMSFYNGV248 RITHQEVDSR258 DWALNGNTLS268 LDEETVIDVP278 EPYNHVSKYC 288 ASLGHKANHS298 FTPNCIYDMF308 VHPRFGPIKC318 IRTLRAVEAD328 EELTVAYGYS 340 PPGKSGPEAP350 EWYQVELKAF360 QAT
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| PDB ID: 4JDS SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [2] |
| PDB Sequence |
HGVCWIYYPD
125 GGSLVGEVNE135 DGEMTGEKIA145 YVYPDERTAL155 YGKFIDGEMI165 EGKLATLMST 175 EEGRPHFELM185 PGNSVYHFDK195 STSSCISTNA205 LLPDPYESER215 VYVAESLISS 225 AGEGLFSKVA235 VGPNTVMSFY245 NGVRITHQEV255 DSRDWALNGN265 TLSLDEETVI 275 DVPEPYNHVS285 KYCASLGHKA295 NHSFTPNCIY305 DMFVHPRFGP315 IKCIRTLRAV 325 EADEELTVAY335 GYDEAPEWYQ354 VELKAFQATQ364 QKHHH
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| PDB ID: 4JLG SETD7 in complex with inhibitor (R)-PFI-2 and S-adenosyl-methionine | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [3] |
| PDB Sequence |
GVCWIYYPDG
126 GSLVGEVNED136 GEMTGEKIAY146 VYPDERTALY156 GKFIDGEMIE166 GKLATLMSTE 176 EGRPHFELMP186 GNSVYHFDKS196 TSSCISTNAL206 LPDPYESERV216 YVAESLISSA 226 GEGLFSKVAV236 GPNTVMSFYN246 GVRITHQEVD256 SRDWALNGNT266 LSLDEETVID 276 VPEPYNHVSK286 YCASLGHKAN296 HSFTPNCIYD306 MFVHPRFGPI316 KCIRTLRAVE 326 ADEELTVAYG336 YDHSPPGKSG346 PEAPEWYQVE356 LKAFQAT
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| PDB ID: 4E47 SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
| PDB Sequence |
HGVCWIYYPD
125 GGSLVGEVNE135 DGEMTGEKIA145 YVYPDERTAL155 YGKFIDGEMI165 EGKLATLMST 175 EEGRPHFELM185 PGNSVYHFDK195 STSSCISTNA205 LLPDPYESER215 VYVAESLISS 225 AGEGLFSKVA235 VGPNTVMSFY245 NGVRITHQEV255 DSRDWALNGN265 TLSLDEETVI 275 DVPEPYNHVS285 KYCASLGHKA295 NHSFTPNCIY305 DMFVHPRFGP315 IKCIRTLRAV 325 EADEELTVAY335 GYDGPEAPEW352 YQVELKAFQA362 TQQKHH
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:223 or .A:225 or .A:226 or .A:227 or .A:228 or .A:245 or .A:264 or .A:265 or .A:282 or .A:293 or .A:294 or .A:295 or .A:296 or .A:297 or .A:298 or .A:335 or .A:352 or .A:356; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 5AYF Crystal structure of SET7/9 in complex with cyproheptadine | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [5] |
| PDB Sequence |
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:223 or .A:224 or .A:225 or .A:226 or .A:227 or .A:228 or .A:245 or .A:264 or .A:265 or .A:282 or .A:293 or .A:294 or .A:295 or .A:296 or .A:297 or .A:335 or .A:352 or .A:356; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 4J83 SET7/9 in complex with TAF10K189A peptide and AdoMet | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [6] |
| PDB Sequence |
GVCWIYYPDG
126 GSLVGEVNED136 GEMTGEKIAY146 VYPDERTALY156 GKFIDGEMIE166 GKLATLMSTE 176 EGRPHFELMP186 GNSVYHFDKS196 TSSCISTNAL206 LPDPYESERV216 YVAESLISSA 226 GEGLFSKVAV236 GPNTVMSFYN246 GVRITHQEVD256 SRDWALNGNT266 LSLDEETVID 276 VPEPYNHVSK286 YCASLGHKAN296 HSFTPNCIYD306 MFVHPRFGPI316 KCIRTLRAVE 326 ADEELTVAYG336 YDHSPPEAPE351 WYQVELKAFQ361 AT
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:223 or .A:224 or .A:225 or .A:226 or .A:227 or .A:228 or .A:245 or .A:264 or .A:265 or .A:282 or .A:293 or .A:294 or .A:295 or .A:296 or .A:297 or .A:335 or .A:352 or .A:356; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| PDB ID: 1N6A Structure of SET7/9 | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [1] |
| PDB Sequence |
HGVCWIYYPD
125 GGSLVGEVNE135 DGETGEKIAY146 VYPDERTALY156 GKFIDGEIEG167 KLATLSTEEG 178 RPHFELPGNS189 VYHFDKSTSS199 CISTNALLPD209 PYESERVYVA219 ESLISSAGEG 229 LFSKVAVGPN239 TVSFYNGVRI250 THQEVDSRDW260 ALNGNTLSLD270 EETVIDVPEP 280 YNHVSKYCAS290 LGHKANHSFT300 PNCIYDFVHP311 RFGPIKCIRT321 LRAVEADEEL 331 TVAYGYPEWY353 QVELKAFQ
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:223 or .A:224 or .A:225 or .A:226 or .A:227 or .A:228 or .A:245 or .A:264 or .A:265 or .A:282 or .A:293 or .A:294 or .A:295 or .A:296 or .A:297 or .A:298 or .A:335 or .A:352 or .A:356; 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 | Mechanism of histone lysine methyl transfer revealed by the structure of SET7/9-AdoMet. EMBO J. 2003 Jan 15;22(2):292-303. | ||||
| REF 2 | SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine | ||||
| REF 3 | (R)-PFI-2 is a potent and selective inhibitor of SETD7 methyltransferase activity in cells. Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12853-8. | ||||
| REF 4 | Setd7 in Complex with Inhibitor and SAM | ||||
| REF 5 | Identification of Cyproheptadine as an Inhibitor of SET Domain Containing Lysine Methyltransferase 7/9 (Set7/9) That Regulates Estrogen-Dependent Transcription. J Med Chem. 2016 Apr 28;59(8):3650-60. | ||||
| REF 6 | Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. J Am Chem Soc. 2013 Oct 16;135(41):15536-48. | ||||
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