Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T00933 | Target Info | |||
| Target Name | Histone lysine demethylase PHF8 (PHF8) | ||||
| Synonyms | ZNF422; PHD finger protein 8; KIAA1111 | ||||
| Target Type | Literature-reported Target | ||||
| Gene Name | PHF8 | ||||
| Biochemical Class | Paired donor oxygen oxidoreductase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: 2-(carboxymethylamino)-2-oxoacetic acid | Ligand Info | |||||
| Structure Description | Structure of PHF8 in complex with histone H3 | PDB:3KV4 | ||||
| Method | X-ray diffraction | Resolution | 2.19 Å | Mutation | No | [1] |
| PDB Sequence |
SVPVYCLCRL
12 PYDVTRFMIE22 CDMCQDWFHG32 SCVGVEEEKA42 ADIDLYHCPN52 CEVLHGPSIM 62 KKKPVKTGSP85 TFVRELRSRT95 FDSSDEVILK105 PTGNQLTVEF115 LEENSFSVPI 125 LVLKKDGLGM135 TLPSPSFTVR145 DVEHYVGSDK155 EIDVIDVTRQ165 ADCKMKLGDF 175 VKYYYSGKRE185 KVLNVISLEF195 SDTRLSNLVE205 TPKIVRKLSW215 VENLWPEECV 225 FERPNVQKYC235 LMSVRDSYTD245 FHIDFGGTSV255 WYHVLKGEKI265 FYLIRPTNAN 275 LTLFECWSSS285 SNQNEMFFGD295 QVDKCYKCSV305 KQGQTLFIPT315 GWIHAVLTPV 325 DCLAFGGNFL335 HSLNIEMQLK345 AYEIEKRLST355 ADLFRFPNFE365 TICWYVGKHI 375 LDIFRGLREN385 RRHPASYLVH395 GGKALNLAFR405 AWTRKEALPD415 HEDEIPETVR 425 TVQLIKDLAR435 EIRLVEDIFQ445 QN
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| Ligand Name: N-Trimethyllysine | Ligand Info | |||||
| Structure Description | Structure of PHF8 in complex with histone H3 | PDB:3KV4 | ||||
| Method | X-ray diffraction | Resolution | 2.19 Å | Mutation | No | [1] |
| PDB Sequence |
SVPVYCLCRL
12 PYDVTRFMIE22 CDMCQDWFHG32 SCVGVEEEKA42 ADIDLYHCPN52 CEVLHGPSIM 62 KKKPVKTGSP85 TFVRELRSRT95 FDSSDEVILK105 PTGNQLTVEF115 LEENSFSVPI 125 LVLKKDGLGM135 TLPSPSFTVR145 DVEHYVGSDK155 EIDVIDVTRQ165 ADCKMKLGDF 175 VKYYYSGKRE185 KVLNVISLEF195 SDTRLSNLVE205 TPKIVRKLSW215 VENLWPEECV 225 FERPNVQKYC235 LMSVRDSYTD245 FHIDFGGTSV255 WYHVLKGEKI265 FYLIRPTNAN 275 LTLFECWSSS285 SNQNEMFFGD295 QVDKCYKCSV305 KQGQTLFIPT315 GWIHAVLTPV 325 DCLAFGGNFL335 HSLNIEMQLK345 AYEIEKRLST355 ADLFRFPNFE365 TICWYVGKHI 375 LDIFRGLREN385 RRHPASYLVH395 GGKALNLAFR405 AWTRKEALPD415 HEDEIPETVR 425 TVQLIKDLAR435 EIRLVEDIFQ445 QN
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| Ligand Name: Daminozide | Ligand Info | |||||
| Structure Description | Crystal Structure of human PHF8 in complex with Daminozide | PDB:4DO0 | ||||
| Method | X-ray diffraction | Resolution | 2.55 Å | Mutation | No | [2] |
| PDB Sequence |
VKTGSPTFVR
89 ELRSRTFDSS99 DEVILKPTGN109 QLTVEFLEEN119 SFSVPILVLK129 KDGLGMTLPS 139 PSFTVRDVEH149 YVGSDKEIDV159 IDVTRQADCK169 MKLGDFVKYY179 YSGKREKVLN 189 VISLEFSDTR199 LSNLVETPKI209 VRKLSWVENL219 WPEECVFERP229 NVQKYCLMSV 239 RDSYTDFHID249 FGGTSVWYHV259 LKGEKIFYLI269 RPTNANLTLF279 ECWSSSSNQN 289 EMFFGDQVDK299 CYKCSVKQGQ309 TLFIPTGWIH319 AVLTPVDCLA329 FGGNFLHSLN 339 IEMQLKAYEI349 EKRLSTADLF359 RFPNFETICW369 YVGKHILDIF379 RGLRENRRHP 389 ASYLVHGGKA399 LNLAFRAWTR409 KEALPDHEDE419 IPETVRTVQL429 IKDLAREIRL 439 VED
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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 .DZA or .DZA2 or .DZA3 or :3DZA;style chemicals stick;color identity;select .A:189 or .A:191 or .A:236 or .A:238 or .A:243 or .A:244 or .A:247 or .A:249 or .A:250 or .A:257 or .A:264 or .A:319 or .A:321 or .A:323 or .A:333; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Alpha-ketoglutaric acid | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic core domain of human PHF8 complexed with alpha-ketoglutarate | PDB:3K3O | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [3] |
| PDB Sequence |
LRSRTFDSSD
100 EVILKPTGNQ110 LTVEFLEENS120 FSVPILVLKK130 DGLGMTLPSP140 SFTVRDVEHY 150 VGSKEIDVID161 VTRQADCKMK171 LGDFVKYYYS181 GKREKVLNVI191 SLEFSDTRLS 201 NLVETPKIVR211 KLSWVENLWP221 EECVFERPNV231 QKYCLMSVRD241 SYTDFHIDFG 251 GTSVWYHVLK261 GEKIFYLIRP271 TNANLTLFEC281 WSSSSNQNEM291 FFGDQVDKCY 301 KCSVKQGQTL311 FIPTGWIHAV321 LTPVDCLAFG331 GNFLHSLNIE341 MQLKAYEIEK 351 RLSFRFPNFE365 TICWYVGKHI375 LDIFRGLREN385 RRHPASYLVH395 GGKALNLAFR 405 AWTRKEALPD415 HEDEIPETVR425 TVQLIKDLAR435 EIRLVEDIFQ445 |
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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 .AKG or .AKG2 or .AKG3 or :3AKG;style chemicals stick;color identity;select .A:189 or .A:191 or .A:236 or .A:238 or .A:244 or .A:247 or .A:249 or .A:257 or .A:264 or .A:266 or .A:319 or .A:321 or .A:323; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Beta-D-Glucose | Ligand Info | |||||
| Structure Description | Crystal structure of the catalytic domain of PHD finger protein 8 | PDB:2WWU | ||||
| Method | X-ray diffraction | Resolution | 2.15 Å | Mutation | No | [4] |
| PDB Sequence |
VKTGSPTFVR
89 ELRSRTFDSS99 DEVILKPTGN109 QLTVEFLEEN119 SFSVPILVLK129 KDGLGMTLPS 139 PSFTVRDVEH149 YVGSDKEIDV159 IDVTRQADCK169 MKLGDFVKYY179 YSGKREKVLN 189 VISLEFSDTR199 LSNLVETPKI209 VRKLSWVENL219 WPEECVFERP229 NVQKYCLMSV 239 RDSYTDFHID249 FGGTSVWYHV259 LKGEKIFYLI269 RPTNANLTLF279 ECWSSSSNQN 289 EMFFGDQVDK299 CYKCSVKQGQ309 TLFIPTGWIH319 AVLTPVDCLA329 FGGNFLHSLN 339 IEMQLKAYEI349 EKRLSTADLF359 RFPNFETICW369 YVGKHILDIF379 RGLRENRRHP 389 ASYLVHGGKA399 LNLAFRAWTR409 KEALPDHEDE419 IPETVRTVQL429 IKDLAREIRL 439 VED
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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 .BGC or .BGC2 or .BGC3 or :3BGC;style chemicals stick;color identity;select .A:179 or .A:180 or .A:181 or .A:182 or .A:184 or .A:239 or .A:246 or .A:247 or .A:248 or .A:279 or .A:282 or .A:283 or .A:288 or .A:326 or .A:350 or .A:353 or .A:354 or .A:355; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N(6),N(6)-Dimethyl-L-lysine | Ligand Info | |||||
| Structure Description | Structure of PHF8 in complex with histone H3 | PDB:3KV4 | ||||
| Method | X-ray diffraction | Resolution | 2.19 Å | Mutation | No | [1] |
| PDB Sequence |
SVPVYCLCRL
12 PYDVTRFMIE22 CDMCQDWFHG32 SCVGVEEEKA42 ADIDLYHCPN52 CEVLHGPSIM 62 KKKPVKTGSP85 TFVRELRSRT95 FDSSDEVILK105 PTGNQLTVEF115 LEENSFSVPI 125 LVLKKDGLGM135 TLPSPSFTVR145 DVEHYVGSDK155 EIDVIDVTRQ165 ADCKMKLGDF 175 VKYYYSGKRE185 KVLNVISLEF195 SDTRLSNLVE205 TPKIVRKLSW215 VENLWPEECV 225 FERPNVQKYC235 LMSVRDSYTD245 FHIDFGGTSV255 WYHVLKGEKI265 FYLIRPTNAN 275 LTLFECWSSS285 SNQNEMFFGD295 QVDKCYKCSV305 KQGQTLFIPT315 GWIHAVLTPV 325 DCLAFGGNFL335 HSLNIEMQLK345 AYEIEKRLST355 ADLFRFPNFE365 TICWYVGKHI 375 LDIFRGLREN385 RRHPASYLVH395 GGKALNLAFR405 AWTRKEALPD415 HEDEIPETVR 425 TVQLIKDLAR435 EIRLVEDIFQ445 QN
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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 .MLY or .MLY2 or .MLY3 or :3MLY;style chemicals stick;color identity;select .A:191 or .A:192 or .A:234 or .A:236 or .A:249 or .A:250 or .A:255 or .A:331 or .A:332 or .A:333 or .A:358 or .A:359; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat Struct Mol Biol. 2010 Jan;17(1):38-43. | ||||
| REF 2 | Crystal Structure of human PHF8 in complex with Daminozide | ||||
| REF 3 | Structural insights into a novel histone demethylase PHF8. Cell Res. 2010 Feb;20(2):166-73. | ||||
| REF 4 | Crystal structure of the PHF8 Jumonji domain, an Nepsilon-methyl lysine demethylase. FEBS Lett. 2010 Feb 19;584(4):825-30. | ||||
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