Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T28887 | Target Info | |||
| Target Name | Histone deacetylase 8 (HDAC8) | ||||
| Synonyms | Histone deacetylase-8; HDACL1; HD8; CDA07 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | HDAC8 | ||||
| Biochemical Class | Carbon-nitrogen hydrolase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | 7-amino-4-methyl-chromen-2-one | Ligand Info | |||
| Canonical SMILES | CC1=CC(=O)OC2=C1C=CC(=C2)N | ||||
| InChI | 1S/C10H9NO2/c1-6-4-10(12)13-9-5-7(11)2-3-8(6)9/h2-5H,11H2,1H3 | ||||
| InChIKey | GLNDAGDHSLMOKX-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 92249 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 3EWF Crystal Structure Analysis of human HDAC8 H143A variant complexed with substrate. | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | Yes | [1] |
| PDB Sequence |
LVPVYIYSPE
23 YVSMCDSLAK33 IPKRASMVHS43 LIEAYALHKQ53 MRIVKPKVAS63 MEEMATFHTD 73 AYLQHLQKVS83 QEGDDDHPDS93 IEYGLGYDCP103 ATEGIFDYAA113 AIGGATITAA 123 QCLIDGMCKV133 AINWSGGWHA143 AKKDEASGFC153 YLNDAVLGIL163 RLRRKFERIL 173 YVDLDLHHGD183 GVEDAFSFTS193 KVMTVSLHKF203 SPGFFPGTGD213 VSDVGLGKGR 223 YYSVNVPIQD233 GIQDEKYYQI243 CESVLKEVYQ253 AFNPKAVVLQ263 LGADTIAGDP 273 MCSFNMTPVG283 IGKCLKYILQ293 WQLATLILGG303 GGYNLANTAR313 CWTYLTGVIL 323 GKTLSSEIPD333 HEFFTAYGPD343 YVLEITPSCR353 PDRNEPHRIQ363 QILNYIKGNL 373 KHVV
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| PDB ID: 4QA5 Crystal structure of A188T/Y306F HDAC8 in complex with a tetrapeptide substrate | ||||||
| Method | X-ray diffraction | Resolution | 1.76 Å | Mutation | Yes | [2] |
| PDB Sequence |
LVPVYIYSPE
23 YVSMCDSLAK33 IPKRASMVHS43 LIEAYALHKQ53 MRIVKPKVAS63 MEEMATFHTD 73 AYLQHLQKVS83 QEGDDDHPDS93 IEYGLGYDCP103 ATEGIFDYAA113 AIGGATITAA 123 QCLIDGMCKV133 AINWSGGWHH143 AKKDEASGFC153 YLNDAVLGIL163 RLRRKFERIL 173 YVDLDLHHGD183 GVEDTFSFTS193 KVMTVSLHKF203 SPGFFPGTGD213 VSDVGLGKGR 223 YYSVNVPIQD233 GIQDEKYYQI243 CESVLKEVYQ253 AFNPKAVVLQ263 LGADTIAGDP 273 MCSFNMTPVG283 IGKCLKYILQ293 WQLATLILGG303 GGFNLANTAR313 CWTYLTGVIL 323 GKTLSSEIPD333 HEFFTAYGPD343 YVLEITPSCR353 PDRNEPHRIQ363 QILNYIKGNL 373 KHVV
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| PDB ID: 4QA6 Crystal structure of I243N/Y306F HDAC8 in complex with a tetrapeptide substrate | ||||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | Yes | [2] |
| PDB Sequence |
LVPVYIYSPE
23 YVSMCDSLAK33 IPKRASMVHS43 LIEAYALHKQ53 MRIVKPKVAS63 MEEMATFHTD 73 AYLQHLQKVS83 QEGDDDHPDS93 IEYGLGYDCP103 ATEGIFDYAA113 AIGGATITAA 123 QCLIDGMCKV133 AINWSGGWHH143 AKKDEASGFC153 YLNDAVLGIL163 RLRRKFERIL 173 YVDLDLHHGD183 GVEDAFSFTS193 KVMTVSLHKF203 SPGFFPGTGD213 VSDVGLGKGR 223 YYSVNVPIQD233 GIQDEKYYQN243 CESVLKEVYQ253 AFNPKAVVLQ263 LGADTIAGDP 273 MCSFNMTPVG283 IGKCLKYILQ293 WQLATLILGG303 GGFNLANTAR313 CWTYLTGVIL 323 GKTLSSEIPD333 HEFFTAYGPD343 YVLEITPSCR353 PDRNEPHRIQ363 QILNYIKGNL 373 KHVV
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| PDB ID: 4QA7 Crystal structure of H334R/Y306F HDAC8 in complex with a tetrapeptide substrate | ||||||
| Method | X-ray diffraction | Resolution | 2.31 Å | Mutation | Yes | [2] |
| PDB Sequence |
SLVPVYIYSP
22 EYVSMCDSLA32 KIPKRASMVH42 SLIEAYALHK52 QMRIVKPKVA62 SMEEMATFHT 72 DAYLQHLQKV82 SQEGDDDHPD92 SIEYGLGYDC102 PATEGIFDYA112 AAIGGATITA 122 AQCLIDGMCK132 VAINWSGGWH142 HAKKDEASGF152 CYLNDAVLGI162 LRLRRKFERI 172 LYVDLDLHHG182 DGVEDAFSFT192 SKVMTVSLHK202 FSPGFFPGTG212 DVSDVGLGKG 222 RYYSVNVPIQ232 DGIQDEKYYQ242 ICESVLKEVY252 QAFNPKAVVL262 QLGADTIAGD 272 PMCSFNMTPV282 GIGKCLKYIL292 QWQLATLILG302 GGGFNLANTA312 RCWTYLTGVI 322 LGKTLSSEIP332 DREFFTAYGP342 DYVLEITPSC352 RPDRNEPHRI362 QQILNYIKGN 372 LKHVV
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Click to Show 3D Structure of This Binding Site
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry. 2008 Dec 23;47(51):13554-63. | ||||
| REF 2 | Compromised structure and function of HDAC8 mutants identified in Cornelia de Lange Syndrome spectrum disorders. ACS Chem Biol. 2014 Sep 19;9(9):2157-64. | ||||
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