Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T68547 | Target Info | |||
| Target Name | Histone deacetylase 1 (HDAC1) | ||||
| Synonyms | RPD3L1; HD1 | ||||
| Target Type | Successful Target | ||||
| Gene Name | HDAC1 | ||||
| Biochemical Class | Carbon-nitrogen hydrolase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | Myo-inositol hexaphosphate | Ligand Info | |||
| Canonical SMILES | C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O | ||||
| InChI | 1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24) | ||||
| InChIKey | IMQLKJBTEOYOSI-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 890 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6Z2J The structure of the dimeric HDAC1/MIDEAS/DNTTIP1 MiDAC deacetylase complex | ||||||
| Method | Electron microscopy | Resolution | 4.00 Å | Mutation | No | [1] |
| PDB Sequence |
RRKVCYYYDG
17 DVGNYYYGQG27 HPMKPHRIRM37 THNLLLNYGL47 YRKMEIYRPH57 KANAEEMTKY 67 HSDDYIKFLR77 SIRPDNMSEY87 SKQMQRFNVG97 EDCPVFDGLF107 EFCQLSTGGS 117 VASAVKLNKQ127 QTDIAVNWAG137 GLHHAKKSEA147 SGFCYVNDIV157 LAILELLKYH 167 QRVLYIDIDI177 HHGDGVEEAF187 YTTDRVMTVS197 FHKYGEYFPG207 TGDLRDIGAG 217 KGKYYAVNYP227 LRDGIDDESY237 EAIFKPVMSK247 VMEMFQPSAV257 VLQCGSDSLS 267 GDRLGCFNLT277 IKGHAKCVEF287 VKSFNLPMLM297 LGGGGYTIRN307 VARCWTYETA 317 VALDTEIPNE327 LPYNDYFEYF337 GPDFKLHISP347 SNMTNQNTNE357 YLEKIKQRLF 367 ENLRMLPHA
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| PDB ID: 7AO8 Structure of the MTA1/HDAC1/MBD2 NURD deacetylase complex | ||||||
| Method | Electron microscopy | Resolution | 4.50 Å | Mutation | No | [2] |
| PDB Sequence |
RRKVCYYYDG
17 DVGNYYYGQG27 HPMKPHRIRM37 THNLLLNYGL47 YRKMEIYRPH57 KANAEEMTKY 67 HSDDYIKFLR77 SIRPDNMSEY87 SKQMQRFNVG97 EDCPVFDGLF107 EFCQLSTGGS 117 VASAVKLNKQ127 QTDIAVNWAG137 GLHHAKKSEA147 SGFCYVNDIV157 LAILELLKYH 167 QRVLYIDIDI177 HHGDGVEEAF187 YTTDRVMTVS197 FHKYGEYFPG207 TGDLRDIGAG 217 KGKYYAVNYP227 LRDGIDDESY237 EAIFKPVMSK247 VMEMFQPSAV257 VLQCGSDSLS 267 GDRLGCFNLT277 IKGHAKCVEF287 VKSFNLPMLM297 LGGGGYTIRN307 VARCWTYETA 317 VALDTEIPNE327 LPYNDYFEYF337 GPDFKLHISP347 SNMTNQNTNE357 YLEKIKQRLF 367 ENLRMLPHA
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| PDB ID: 5ICN HDAC1:MTA1 in complex with inositol-6-phosphate and a novel peptide inhibitor based on histone H4 | ||||||
| Method | X-ray diffraction | Resolution | 3.30 Å | Mutation | No | [3] |
| PDB Sequence |
RRKVCYYYDG
17 DVGNYYYGQG27 HPMKPHRIRM37 THNLLLNYGL47 YRKMEIYRPH57 KANAEEMTKY 67 HSDDYIKFLR77 SIRPDNMSEY87 SKQMQRFNVG97 EDCPVFDGLF107 EFCQLSTGGS 117 VASAVKLNKQ127 QTDIAVNWAG137 GLHHAKKSEA147 SGFCYVNDIV157 LAILELLKYH 167 QRVLYIDIDI177 HHGDGVEEAF187 YTTDRVMTVS197 FHKYGEYFPG207 TGDLRDIGAG 217 KGKYYAVNYP227 LRDGIDDESY237 EAIFKPVMSK247 VMEMFQPSAV257 VLQCGSDSLS 267 GDRLGCFNLT277 IKGHAKCVEF287 VKSFNLPMLM297 LGGGGYTIRN307 VARCWTYETA 317 VALDTEIPNE327 LPYNDYFEYF337 GPDFKLHISP347 SNMTNQNTNE357 YLEKIKQRLF 367 ENLRMLPHA
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure. Nat Commun. 2020 Jun 26;11(1):3252. | ||||
| REF 2 | The topology of chromatin-binding domains in the NuRD deacetylase complex. Nucleic Acids Res. 2020 Dec 16;48(22):12972-12982. | ||||
| REF 3 | Insights into the activation mechanism of class I HDAC complexes by inositol phosphates. Nat Commun. 2016 Apr 25;7:11262. | ||||
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