Binding Site Information of Target
| 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 | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Cyproheptadine | Ligand Info | |||||
| Structure Description | Crystal structure of SET7/9 in complex with cyproheptadine | PDB:5AYF | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [1] |
| PDB Sequence |
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| Ligand Name: Ademetionine | Ligand Info | |||||
| Structure Description | Structure of SET7/9 | PDB:1N6A | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [2] |
| 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 View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (R)-PFI-2 | Ligand Info | |||||
| Structure Description | SETD7 in complex with inhibitor (R)-PFI-2 and S-adenosyl-methionine | PDB:4JLG | ||||
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1L8 or .1L82 or .1L83 or :31L8;style chemicals stick;color identity;select .A:245 or .A:252 or .A:255 or .A:256 or .A:263 or .A:264 or .A:265 or .A:266 or .A:267 or .A:268 or .A:274 or .A:305 or .A:335 or .A:336 or .A:337 or .A:338 or .A:339 or .A:340 or .A:341; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Sinefungin | Ligand Info | |||||
| Structure Description | Set7/9-ER-Sinefungin complex | PDB:3CBP | ||||
| Method | X-ray diffraction | Resolution | 1.42 Å | Mutation | No | [4] |
| 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 YDHEAPEWYQ354 VELKAFQAT
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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 .SFG or .SFG2 or .SFG3 or :3SFG;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:229 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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ILE223
3.735
SER224
4.483
SER225
4.026
ALA226
2.614
GLY227
3.925
GLU228
2.728
GLY229
4.977
TYR245
4.632
GLY264
3.275
ASN265
2.679
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: N-[(2r)-3-(3-Cyanophenyl)-1-Oxo-1-(Pyrrolidin-1-Yl)propan-2-Yl]-8-Fluoro-1,2,3,4-Tetrahydroisoquinoline-6-Sulfonamide | Ligand Info | |||||
| Structure Description | SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine | PDB:4JDS | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [5] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1L4 or .1L42 or .1L43 or :31L4;style chemicals stick;color identity;select .A:245 or .A:252 or .A:255 or .A:256 or .A:263 or .A:264 or .A:265 or .A:266 or .A:267 or .A:268 or .A:274 or .A:305 or .A:335 or .A:336 or .A:337; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (R)-(3-(3-Cyanophenyl)-1-Oxo-1-(Pyrrolidin-1-Yl)propan-2-Yl)-1,2,3,4-Tetrahydroisoquinoline-6-Sulfonamide | Ligand Info | |||||
| Structure Description | 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 | PDB:4E47 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [6] |
| 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 .0N6 or .0N62 or .0N63 or :30N6;style chemicals stick;color identity;select .A:245 or .A:252 or .A:255 or .A:256 or .A:263 or .A:264 or .A:265 or .A:266 or .A:267 or .A:268 or .A:274 or .A:305 or .A:335 or .A:336 or .A:337; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(1-Methylpiperidin-4-ylidene)tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,9,12,14-heptaen-6-ol | Ligand Info | |||||
| Structure Description | Crystal structure of SET7/9 in complex with a cyproheptadine derivative | PDB:5YLT | ||||
| Method | X-ray diffraction | Resolution | 1.69 Å | Mutation | No | [7] |
| PDB Sequence |
RHGVCWIYYP
124 DGGSLVGEVN134 EDGEMTGEKI144 AYVYPDERTA154 LYGKFIDGEM164 IEGKLATLMS 174 TEEGRPHFEL184 MPGNSVYHFD194 KSTSSCISTN204 ALLPDPYESE214 RVYVAESLIS 224 SAGEGLFSKV234 AVGPNTVMSF244 YNGVRITHQE254 VDSRDWALNG264 NTLSLDEETV 274 IDVPEPYNHV284 SKYCASLGHK294 ANHSFTPNCI304 YDMFVHPRFG314 PIKCIRTLRA 324 VEADEELTVA334 YGYDHSPPGK344 SAPEWYQVEL357 KAFQATQ
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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 .C7N or .C7N2 or .C7N3 or :3C7N;style chemicals stick;color identity;select .A:245 or .A:260 or .A:263 or .A:264 or .A:265 or .A:266 or .A:267 or .A:305 or .A:335 or .A:336 or .A:337 or .A:338 or .A:340 or .A:341 or .A:342 or .A:350 or .A:352 or .A:353; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5'-{[(3s)-3-Amino-3-Carboxypropyl][2-(Hexylamino)ethyl]amino}-5'-Deoxyadenosine | Ligand Info | |||||
| Structure Description | Crystal structure of histone methyltransferase SET7/9 in complex with DAAM-3 | PDB:3VV0 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [8] |
| 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 GYPEWYQVEL357 KAFQA
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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 .KH3 or .KH32 or .KH33 or :3KH3;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:229 or .A:245 or .A:264 or .A:265 or .A:266 or .A:267 or .A:282 or .A:293 or .A:294 or .A:295 or .A:296 or .A:297 or .A:298 or .A:305 or .A:335 or .A:337 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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ILE223
3.473
SER224
4.350
SER225
3.842
ALA226
2.766
GLY227
3.838
GLU228
2.427
GLY229
4.665
TYR245
3.142
GLY264
3.108
ASN265
2.965
THR266
3.136
LEU267
3.557
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| Ligand Name: 5'-{[(3s)-3-Amino-3-Carboxypropyl](Hexyl)amino}-5'-Deoxyadenosine | Ligand Info | |||||
| Structure Description | Crystal structure of histone methyltransferase SET7/9 in complex with AAM-1 | PDB:3VUZ | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [8] |
| PDB Sequence |
GSSGSSGHGV
118 CWIYYPDGGS128 LVGEVNEDGE138 MTGEKIAYVY148 PDERTALYGK158 FIDGEMIEGK 168 LATLMSTEEG178 RPHFELMPGN188 SVYHFDKSTS198 SCISTNALLP208 DPYESERVYV 218 AESLISSAGE228 GLFSKVAVGP238 NTVMSFYNGV248 RITHQEVDSR258 DWALNGNTLS 268 LDEETVIDVP278 EPYNHVSKYC288 ASLGHKANHS298 FTPNCIYDMF308 VHPRFGPIKC 318 IRTLRAVEAD328 EELTVAYGYD338 HEAPEWYQVE356 LKAFQA
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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 .K15 or .K152 or .K153 or :3K15;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:229 or .A:245 or .A:264 or .A:265 or .A:266 or .A:267 or .A:282 or .A:293 or .A:294 or .A:295 or .A:296 or .A:297 or .A:305 or .A:335 or .A:337 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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ILE223
3.630
SER224
4.425
SER225
3.662
ALA226
2.920
GLY227
4.186
GLU228
2.410
GLY229
4.674
TYR245
3.099
GLY264
3.205
ASN265
3.120
THR266
3.264
LEU267
4.861
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| Ligand Name: Selenomethionine | Ligand Info | |||||
| Structure Description | Structure of SET7/9 | PDB:1N6A | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [2] |
| 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 .MSE or .MSE2 or .MSE3 or :3MSE;style chemicals stick;color identity;select .A:119 or .A:121 or .A:125 or .A:129 or .A:130 or .A:131 or .A:132 or .A:133 or .A:134 or .A:137 or .A:138 or .A:140 or .A:141 or .A:144 or .A:155 or .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:165 or .A:166 or .A:167 or .A:169 or .A:170 or .A:171 or .A:172 or .A:174 or .A:175 or .A:181 or .A:182 or .A:183 or .A:184 or .A:186 or .A:187 or .A:191 or .A:192 or .A:193 or .A:211 or .A:212 or .A:215 or .A:216 or .A:232 or .A:234 or .A:236 or .A:240 or .A:241 or .A:243 or .A:244 or .A:269 or .A:270 or .A:305 or .A:306 or .A:308 or .A:309 or .A:311 or .A:312 or .A:316 or .A:317 or .A:318 or .A:319 or .A:320 or .A:321 or .A:325 or .A:331; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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CYS119
4.419
ILE121
4.584
ASP125
3.800
LEU129
4.358
VAL130
4.043
GLY131
3.037
GLU132
3.948
VAL133
3.392
ASN134
4.854
GLY137
4.486
GLU138
1.330
THR140
1.330
GLY141
4.334
ILE144
4.110
LEU155
3.645
LYS158
3.824
PHE159
3.464
ILE160
3.697
ASP161
3.121
GLY162
2.943
GLU163
1.329
ILE165
1.331
GLU166
3.736
GLY167
3.846
LEU169
2.927
ALA170
4.024
THR171
3.118
LEU172
1.329
SER174
1.328
THR175
4.813
HIS181
2.850
PHE182
4.492
GLU183
3.042
LEU184
1.331
PRO186
1.340
GLY187
3.500
TYR191
3.692
HIS192
3.564
PHE193
2.815
TYR211
4.655
GLU212
3.832
ARG215
3.644
VAL216
3.605
SER232
3.193
VAL234
4.542
VAL236
3.911
THR240
3.332
VAL241
1.330
SER243
1.326
PHE244
4.705
LEU269
3.580
ASP270
4.880
TYR305
4.622
ASP306
1.330
PHE308
1.330
VAL309
4.550
PRO311
3.742
ARG312
4.064
ILE316
3.726
LYS317
3.120
CYS318
4.249
ILE319
2.799
ARG320
4.621
THR321
3.614
VAL325
4.495
LEU331
4.050
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | 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 2 | Mechanism of histone lysine methyl transfer revealed by the structure of SET7/9-AdoMet. EMBO J. 2003 Jan 15;22(2):292-303. | ||||
| 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 | Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase. Mol Cell. 2008 May 9;30(3):336-47. | ||||
| REF 5 | SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine | ||||
| REF 6 | Setd7 in Complex with Inhibitor and SAM | ||||
| REF 7 | Development of Novel Inhibitors for Histone Methyltransferase SET7/9 based on Cyproheptadine. ChemMedChem. 2018 Aug 10;13(15):1530-1540. | ||||
| REF 8 | Structures of histone methyltransferase SET7/9 in complexes with adenosylmethionine derivatives. Acta Crystallogr D Biol Crystallogr. 2013 Apr;69(Pt 4):595-602. | ||||
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