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 | Vorinostat | Ligand Info | |||
| Canonical SMILES | C1=CC=C(C=C1)NC(=O)CCCCCCC(=O)NO | ||||
| InChI | 1S/C14H20N2O3/c17-13(15-12-8-4-3-5-9-12)10-6-1-2-7-11-14(18)16-19/h3-5,8-9,19H,1-2,6-7,10-11H2,(H,15,17)(H,16,18) | ||||
| InChIKey | WAEXFXRVDQXREF-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 5311 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1T69 Crystal Structure of human HDAC8 complexed with SAHA | ||||||
| Method | X-ray diffraction | Resolution | 2.91 Å | Mutation | No | [1] |
| PDB Sequence |
LVPVYIYSPE
23 YVSMCDSLAK33 IPKRASMVHS43 LIEAYALHKQ53 MRIVKPKVAS63 MEEMATFHTD 73 AYLQHLQKVS83 QPDSIEYGLG99 YDCPATEGIF109 DYAAAIGGAT119 ITAAQCLIDG 129 MCKVAINWSG139 GWHHAKKDEA149 SGFCYLNDAV159 LGILRLRRKF169 ERILYVDLDL 179 HHGDGVEDAF189 SFTSKVMTVS199 LHKFSPGFFP209 GTGDVSDVGL219 GKGRYYSVNV 229 PIQDGIQDEK239 YYQICESVLK249 EVYQAFNPKA259 VVLQLGADTI269 AGDPMCSFNM 279 TPVGIGKCLK289 YILQWQLATL299 ILGGGGYNLA309 NTARCWTYLT319 GVILGKTLSS 329 EIPDHEFFTA339 YGPDYVLEIT349 PSCRPDRNEP359 HRIQQILNYI369 KGNLKHVV |
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| PDB ID: 7JVU Crystal structure of human histone deacetylase 8 (HDAC8) I45T mutation complexed with SAHA | ||||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | Yes | [2] |
| PDB Sequence |
LVPVYIYSPE
23 YVSMCDSLAK33 IPKRASMVHS43 LTEAYALHKQ53 MRIVKPKVAS63 MEEMATFHTD 73 AYLQHLQKVS83 QEGDDDHPDS93 IEYGLGYDCP103 ATEGIFDYAA113 AIGGATITAA 123 QCLIDGMCKV133 AINWSGGWHH143 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 KHVVI
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| PDB ID: 4QA0 Crystal structure of C153F HDAC8 in complex with SAHA | ||||||
| Method | X-ray diffraction | Resolution | 2.24 Å | Mutation | Yes | [3] |
| PDB Sequence |
LVPVYIYSPE
23 YVSMCDSLAK33 IPKRASMVHS43 LIEAYALHKQ53 MRIVKPKVAS63 MEEMATFHTD 73 AYLQHLQKVS83 QEGDDDHPDS93 IEYGLGYDCP103 ATEGIFDYAA113 AIGGATITAA 123 QCLIDGMCKV133 AINWSGGWHH143 AKKDEASGFF153 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 KHVVIEGRGS383 H
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| PDB ID: 4QA2 Crystal structure of I243N HDAC8 in complex with SAHA | ||||||
| Method | X-ray diffraction | Resolution | 2.38 Å | Mutation | Yes | [3] |
| PDB Sequence |
LVPVYIYSPE
23 YVSMCDSLAK33 IPKRASMVHS43 LIEAYALHKQ53 MRIVKPKVAS63 MEEMATFHTD 73 AYLQHLQKVS83 QEGYGLGYDC102 PATEGIFDYA112 AAIGGATITA122 AQCLIDGMCK 132 VAINWSGGWH142 HAKKDEASGF152 CYLNDAVLGI162 LRLRRKFERI172 LYVDLDLHHG 182 DGVEDAFSFT192 SKVMTVSLHK202 FSPGFFPGTG212 DVSDVGLGKG222 RYYSVNVPIQ 232 DGIQDEKYYQ242 NCESVLKEVY252 QAFNPKAVVL262 QLGADTIAGD272 PMCSFNMTPV 282 GIGKCLKYIL292 QWQLATLILG302 GGGYNLANTA312 RCWTYLTGVI322 LGKTLSSEIP 332 DHEFFTAYGP342 DYVLEITPSC352 RPDRNEPHRI362 QQILNYIKGN372 LKHVVI |
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure. 2004 Jul;12(7):1325-34. | ||||
| REF 2 | Structural analysis of histone deacetylase 8 mutants associated with Cornelia de Lange Syndrome spectrum disorders. J Struct Biol. 2021 Mar;213(1):107681. | ||||
| REF 3 | 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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